DGVfrequency {nanotatoR} | R Documentation |
Frequency calculation of variants compared to DGV.
DGVfrequency( hgpath, smap, smap_data, win_indel_DGV = 10000, win_inv_trans_DGV = 50000, perc_similarity_DGV = 0.5, input_fmt_SV = c("Text", "dataframe"), returnMethod = c("Text", "dataFrame"), outpath, EnzymeType = c("SVMerge", "SE") )
hgpath |
character. Path to Database of Genomic Variants (DGV) Text file. |
smap |
character. File name for smap textfile. |
smap_data |
dataframe. Dataset containing smap data. |
win_indel_DGV |
Numeric. Insertion and deletion error window.Default 10000 bases. |
win_inv_trans_DGV |
Numeric. Inversion and translocation error window. Default 50000 bases. |
perc_similarity_DGV |
Numeric . ThresholdPercentage similarity of the query SV and reference SV. Default 0.5. |
input_fmt_SV |
boolean . Options Text and dataframe. |
returnMethod |
character. Choice between text or data frame as the output. |
outpath |
character. Path where gene lists are saved. |
EnzymeType |
boolean . Options SE and SVMerge. |
Text and character vector containg gene list and terms associated with them are stored as text files.
hgpath=system.file("extdata", "GRCh37_hg19_variants_2016-05-15.txt", package="nanotatoR") smappath=system.file("extdata", "GM24385_Ason_DLE1_VAP_trio5.smap", package="nanotatoR") datDGV <- DGVfrequency (hgpath = hgpath, smap = smappath, win_indel_DGV = 10000, EnzymeType = "SE", input_fmt_SV = "Text", perc_similarity_DGV = 0.5,returnMethod="dataFrame")