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* checking for file ‘ISAnalytics/DESCRIPTION’ ... OK
* preparing ‘ISAnalytics’:
* checking DESCRIPTION meta-information ... OK
* installing the package to process help pages
* building the PDF package manual
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\T1/ptm/m/n/10 For more de-tails on how to use this func-tion: \T1/zi4/m/n/10 v
ignette("Working with aggregate functions",package
[2] [3] (/usr/local/texlive/2020/texmf-dist/tex/latex/psnfss/ts1ptm.fd)
[4] [5] [6]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[7]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
[8]
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[] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto
-oncogene.tsv.xz", package[]
[9] [10] [11]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
[12]
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[13]
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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\T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion
types (ob-tained via [][]com-
[14] [15] [16]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 sample_statistics[][][]()\T1/ptm/m/n/10 ,
[17]
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
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\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,
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\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[18]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[19]
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[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[20] [21]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_auto[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_interactive[][][]()\T1/ptm/m/n/10 ,
[22]
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[]\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i
n \T1/zi4/m/n/10 quantification_types()
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
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\T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f
er to the vi-gnette - vi-gnette("how_to_import_functions")
[23]
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[][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10
https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm
l$[][]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_interactive[][][]()\T1/ptm/m/n/10 ,
[24]
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[]\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i
n \T1/zi4/m/n/10 quantification_types()
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
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\T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f
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[25]
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n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
[27] [28]
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
[29]
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive
[30]
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[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions
[31] [32]
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\T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z
i4/m/n/10 vignette("Collision removal functionality",package
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[35]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[36]
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
[37] [38]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[39]
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[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
[40]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
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\T1/ptm/m/n/10 For more de-tails on how to use this func-tion: \T1/zi4/m/n/10 v
ignette("Working with aggregate functions",package
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[7]
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[8]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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[] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto
-oncogene.tsv.xz", package[]
[9] [10] [11]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[12]
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[13]
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
[14]
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\T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion
types (ob-tained via [][]com-
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 sample_statistics[][][]()\T1/ptm/m/n/10 ,
[17]
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
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\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,
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\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[20]
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[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_auto[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_interactive[][][]()\T1/ptm/m/n/10 ,
[23]
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[]\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i
n \T1/zi4/m/n/10 quantification_types()
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
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\T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f
er to the vi-gnette - vi-gnette("how_to_import_functions")
[24]
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[][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10
https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm
l$[][]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_interactive[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i
n \T1/zi4/m/n/10 quantification_types()
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
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\T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
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[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions
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\T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z
i4/m/n/10 vignette("Collision removal functionality",package
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
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\T1/ptm/m/n/10 For more de-tails on how to use this func-tion: \T1/zi4/m/n/10 v
ignette("Working with aggregate functions",package
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[7]
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[8]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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[] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto
-oncogene.tsv.xz", package[]
[9] [10] [11]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[12]
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[13]
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separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
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[14]
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\T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion
types (ob-tained via [][]com-
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 sample_statistics[][][]()\T1/ptm/m/n/10 ,
[17]
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
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\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,
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\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
[18] [19]
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[20]
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[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[21]
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[22]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_auto[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_interactive[][][]()\T1/ptm/m/n/10 ,
[23]
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[]\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i
n \T1/zi4/m/n/10 quantification_types()
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
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\T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f
er to the vi-gnette - vi-gnette("how_to_import_functions")
[24]
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[][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10
https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm
l$[][]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_interactive[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
[27] [28] [29]
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
[30]
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
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[31]
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[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions
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\T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z
i4/m/n/10 vignette("Collision removal functionality",package
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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[36]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[37]
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
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, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[40]
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[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
[41]
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, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
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[]| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 ,
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[]| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 For more de-tails on how to use this func-tion: \T1/zi4/m/n/10 v
ignette("Working with aggregate functions",package
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[7]
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[8]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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[] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto
-oncogene.tsv.xz", package[]
[9] [10] [11]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[12]
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
/m/n/10 aggregate_values_by_key()\T1/ptm/m/n/10 )
[13]
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
[14]
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\T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion
types (ob-tained via [][]com-
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 sample_statistics[][][]()\T1/ptm/m/n/10 ,
[17]
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
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\T1/ptm/m/it/10 ram-e-ter in \T1/zi4/m/n/10 import_association_file\T1/ptm/m/it
/10 ,
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\T1/zi4/m/n/10 import_parallel_vispa2Matrices_interactive \T1/ptm/m/it/10 and
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[20]
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[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[21]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_auto[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_interactive[][][]()\T1/ptm/m/n/10 ,
[23]
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[]\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i
n \T1/zi4/m/n/10 quantification_types()
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
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\T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f
er to the vi-gnette - vi-gnette("how_to_import_functions")
[24]
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[][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10
https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm
l$[][]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_interactive[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i
n \T1/zi4/m/n/10 quantification_types()
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
ional named ar-gu-ments to pass to \T1/zi4/m/n/10 ìmport_association_file
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\T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
[30]
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
antification_type \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel
_vispa2Matrices_interactive
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[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions
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\T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z
i4/m/n/10 vignette("Collision removal functionality",package
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[40]
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[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
[41]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
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[]| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_auto\T1/ptm/m/n/10 ,
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[]| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 ,
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[]| \T1/zi4/m/n/10 clinical_relevant_suspicious_genes\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 ,
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\T1/ptm/m/n/10 For more de-tails on how to use this func-tion: \T1/zi4/m/n/10 v
ignette("Working with aggregate functions",package
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 generate_Vispa2_
launch_AF[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association
_file[][][]()\T1/ptm/m/n/10 ,
[7]
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\T1/zi4/m/n/10 ashpublications . org / blood / article / 117 / 20 / 5332 / 2120
6 / Lentiviral-[]vector-[]common-[]integration-[]sites-[]in$[][]
[8]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 comparison_mat
rix[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm
/m/n/10 , [][]\T1/zi4/m/n/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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[] \T1/zi4/m/n/10 onco_db_file = system.file("extdata", "201806_uniprot-Proto
-oncogene.tsv.xz", package[]
[9] [10] [11]
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[]\T1/ptm/m/n/10 A named list of in-te-gra-tion ma-tri-ces, ide-ally ob-tained
via [][]im-port_parallel_Vispa2Matrices_interactive[][][]
[12]
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
ilter[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 top_integrations[][][]()
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[]\T1/ptm/m/n/10 An in-te-gra-tion ma-trix - aka a data frame that in-cludes th
e \T1/zi4/m/n/10 mandatory_IS_vars()
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\T1/ptm/m/n/10 as columns. The ma-trix can ei-ther be ag-gre-gated (via \T1/zi4
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[][]\T1/zi4/m/n/10 sample_statistics[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
separate_quant_matrices[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 threshold_f
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\T1/ptm/m/n/10 value columns cor-re-spond-ing to dif-fer-ent quan-tifi-ca-tion
types (ob-tained via [][]com-
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 sample_statistics[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/it/10 Possible choices for the \T1/zi4/m/n/10 dates_format \T1/ptm/
m/it/10 pa-
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/10 ,
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unzip_file_system[][][]()
[20]
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[]\T1/ptm/m/n/10 You cor-reclty type names in cor-re-spond-ing po-si-tions, for
ex-am-ple c("CLOEXP", "PROJECT1100",
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_auto[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_V
ispa2Matrices_interactive[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 A vec-tor of re-quested quan-tifi-ca-tion_types. Must be one i
n \T1/zi4/m/n/10 quantification_types()
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[]\T1/ptm/m/n/10 <[][]\T1/zi4/m/n/10 dynamic-dots[][][]\T1/ptm/m/n/10 > Ad-di-t
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\T1/ptm/m/n/10 For more de-tails on how to prop-erly use these func-tions, re-f
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[24]
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[][][]\T1/zi4/m/n/10 matching_options[][][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10
https : / / stringr . tidyverse . org / articles / regular-[]expressions . htm
l$[][]
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Other Im-port func-tions: [][]\T1/zi4/m/n/10 import_associatio
n_file[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 import_parallel_Vispa2Matrice
s_auto[][][]()\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 ma
tching_opt \T1/ptm/m/n/10 pa-ram-e-ter in \T1/zi4/m/n/10 import_parallel_vispa2
Matrices_auto\T1/ptm/m/n/10 .
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[]\T1/ptm/m/n/10 These are all the pos-si-ble val-ues for the \T1/zi4/m/n/10 qu
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[]\T1/ptm/m/n/10 The se-quence count ma-trix al-ready pro-cessed for col-li-sio
ns via \T1/zi4/m/n/10 remove_collisions
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\T1/ptm/m/n/10 tails on how to use col-li-sion re-moval func-tion-al-ity: \T1/z
i4/m/n/10 vignette("Collision removal functionality",package
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[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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\T1/ptm/m/n/10 nu-meric vec-tor for \T1/zi4/m/n/10 threshold \T1/ptm/m/n/10 and
char-ac-ter vec-tors for both \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 an
d \T1/zi4/m/n/10 comparators\T1/ptm/m/n/10 .
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\T1/ptm/m/n/10 A fil-ter-ing con-di-tion is ob-tained by com-bin-ing el-e-ment
by el-e-ment \T1/zi4/m/n/10 cols_to_compare \T1/ptm/m/n/10 + \T1/zi4/m/n/10 com
parators
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
/10 cumulative_count_union[][][]()\T1/ptm/m/n/10 ,
[40]
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[]\T1/zi4/m/n/10 keep = "nothing" \T1/ptm/m/n/10 only keeps the manda-tory colu
mns (\T1/zi4/m/n/10 mandatory_IS_vars()\T1/ptm/m/n/10 ) plus the columns
[41]
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[]\T1/ptm/m/n/10 Other Anal-y-sis func-tions: [][]\T1/zi4/m/n/10 CIS_grubbs[][]
[]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 comparison_matrix[][][]()\T1/ptm/m/n/10
, [][]\T1/zi4/m/n/10 compute_abundance[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n
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[]\T1/ptm/m/n/10 Other Util-ity func-tions: [][]\T1/zi4/m/n/10 as_sparse_matrix
[][][]()\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_Vispa2_launch_AF[][][]()\T
1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 generate_blank_association_file[][][]()
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[]| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_auto\T1/ptm/m/n/10 ,
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[]| \T1/zi4/m/n/10 import_parallel_Vispa2Matrices_interactive\T1/ptm/m/n/10 ,
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Output written on Rd2.pdf (45 pages, 187651 bytes).
Transcript written on Rd2.log.
Saving output to ‘/private/tmp/RtmpQ06Mw4/Rbuild131794b17d8fa/ISAnalytics/build/ISAnalytics.pdf’ ...
Done
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘ISAnalytics_1.0.11.tar.gz’
