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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data rDGIdb
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* checking for file ‘rDGIdb/DESCRIPTION’ ... OK
* preparing ‘rDGIdb’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘vignette.Rnw’ using knitr
queryDGIdb package:rDGIdb R Documentation
_Q_u_e_r_y _D_G_I_d_b _u_s_i_n_g _R
_D_e_s_c_r_i_p_t_i_o_n:
Provides an interface to query DGIdb from within R using the DGIdb
API. The function is implemented to reflect the as good as
possible the web-interface.
_U_s_a_g_e:
queryDGIdb(genes,
sourceDatabases = NULL,
geneCategories = NULL,
interactionTypes = NULL)
_A_r_g_u_m_e_n_t_s:
genes: A character vector of genes for which drug interactions are
queried.
sourceDatabases: A character vector of source databases to be queried.
To query all available databases, skip argument or use
'NULL'. To see available options, type 'sourceDatabases()'.
geneCategories: A character vector of gene categories to be queried. To
query for all gene categories, skip argument or use 'NULL'.
To see available options, type 'geneCategories()'.
interactionTypes: A character vector of interaction types to be
queried. To query for all interaction types, skip argument or
use 'NULL'. To see available options, type
'interactionTypes()'.
_D_e_t_a_i_l_s:
Only the first argument ('genes') is required, all other arguments
are optional. When optional arguments are not provided, the query
considers all available possibilities for optional arguments:
'sourceDatabases', 'geneCategories', and 'interactionTypes'.
_V_a_l_u_e:
A S4 object of type 'rDGIdbResult'.
_A_u_t_h_o_r(_s):
Thomas Thurnherr <thomas.thurnherr@gmail.com>
_R_e_f_e_r_e_n_c_e_s:
Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL,
Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR,
Wilson RK, Mardis ER, Griffith M, Griffith OL. DGIdb 2.0: mining
clinically relevant drug-gene interactions. Nucleic Acids
Research. 2016 Jan 4;44(D1):D1036-44. doi:10.1093/nar/gkv1165.
_S_e_e _A_l_s_o:
'rDGIdbResult', 'rDGIdbFilters', 'plotInteractionsBySource'
_E_x_a_m_p_l_e_s:
genes <- c("XYZA", "TNF", "IL6", "IL8")
result <- queryDGIdb(genes = genes)
result <- queryDGIdb(genes = genes,
sourceDatabases = c("MyCancerGenome","TEND","TTD"),
geneCategories = "CELL SURFACE",
interactionTypes = c("activator","inhibitor"))
rDGIdbFilters package:rDGIdb R Documentation
_F_i_l_t_e_r _o_p_t_i_o_n_s _f_o_r _r_D_G_I_d_b _q_u_e_r_i_e_s.
_D_e_s_c_r_i_p_t_i_o_n:
The gene categories, interaction types, and source databases
available to filter queries with 'queryDGIdb'.
_U_s_a_g_e:
geneCategories()
interactionTypes()
sourceDatabases()
_V_a_l_u_e:
'geneCategories' returns a character vector of available gene
categories which can be used to filter DGIdb queries with
'queryDGIdb'.
'interactionTypes' returns a character vector of available
interaction types which can be used to filter DGIdb queries with
'queryDGIdb'.
'sourceDatabases' returns a character vector of available source
databases which can be used to filter DGIdb queries with
'queryDGIdb'.
_A_u_t_h_o_r(_s):
Thomas Thurnherr <thomas.thurnherr@gmail.com>
_R_e_f_e_r_e_n_c_e_s:
Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL,
Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR,
Wilson RK, Mardis ER, Griffith M, Griffith OL. DGIdb 2.0: mining
clinically relevant drug-gene interactions. Nucleic Acids
Research. 2016 Jan 4;44(D1):D1036-44. doi:10.1093/nar/gkv1165.
_S_e_e _A_l_s_o:
'queryDGIdb', 'rDGIdbResult', 'plotInteractionsBySource'
_E_x_a_m_p_l_e_s:
geneCategories()
interactionTypes()
sourceDatabases()
res <- queryDGIdb(genes = "AP1",
interactionTypes = NULL,
geneCategories = NULL,
sourceDatabases = NULL)
rDGIdbResult package:rDGIdb R Documentation
_R_e_s_u_l_t _o_b_j_e_c_t _o_f _a _r_D_G_I_d_b _q_u_e_r_y
_D_e_s_c_r_i_p_t_i_o_n:
S4 helper functions to access DGIdb results, formatted in a
similar way as result tables on the DGIdb web interface.
_U_s_a_g_e:
## S4 method for signature 'rDGIdbResult'
resultSummary(object)
## S4 method for signature 'rDGIdbResult'
detailedResults(object)
## S4 method for signature 'rDGIdbResult'
byGene(object)
## S4 method for signature 'rDGIdbResult'
searchTermSummary(object)
_A_r_g_u_m_e_n_t_s:
object: A 'rDGIdbResult' object returned by 'queryDGIdb'.
_V_a_l_u_e:
'resultSummary' returns a 'data.frame' that summarizes drug-gene
interactions by the source(s) that reported them.
'detailedResult' returns a 'data.frame' with search terms matching
exactly one gene that has one or more drug interactions.
'byGene' returns a 'data.frame' with drug interaction count and
druggable categories associated with each gene.
'searchTermSummary' returns a 'data.frame' that summarizes the
attempt to map gene names supplied by the user to gene records in
DGIdb.
_A_u_t_h_o_r(_s):
Thomas Thurnherr <thomas.thurnherr@gmail.com>
_R_e_f_e_r_e_n_c_e_s:
Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL,
Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR,
Wilson RK, Mardis ER, Griffith M, Griffith OL. DGIdb 2.0: mining
clinically relevant drug-gene interactions. Nucleic Acids
Research. 2016 Jan 4;44(D1):D1036-44. doi:10.1093/nar/gkv1165.
_S_e_e _A_l_s_o:
'queryDGIdb', 'rDGIdbFilters', 'plotInteractionsBySource'
_E_x_a_m_p_l_e_s:
genes <- c("XYZA", "TNF", "IL6", "IL8")
result <- queryDGIdb(genes = genes)
resultSummary(result)
detailedResults(result)
byGene(result)
searchTermSummary(result)
plotInteractionsBySource package:rDGIdb R Documentation
_I_n_t_e_r_a_c_t_i_o_n_s _b_y _s_o_u_r_c_e
_D_e_s_c_r_i_p_t_i_o_n:
Creates a plot to visualize the number of interactions per source.
_U_s_a_g_e:
plotInteractionsBySource(queryResult, ...)
_A_r_g_u_m_e_n_t_s:
queryResult: A 'rDGIdbResult' object obtained from 'queryDGIdb'.
...: Other arguments passed to barplot.
_V_a_l_u_e:
A plot is created on the current graphics device.
_A_u_t_h_o_r(_s):
Thomas Thurnherr <thomas.thurnherr@gmail.com>
_R_e_f_e_r_e_n_c_e_s:
Wagner AH, Coffman AC, Ainscough BJ, Spies NC, Skidmore ZL,
Campbell KM, Krysiak K, Pan D, McMichael JF, Eldred JM, Walker JR,
Wilson RK, Mardis ER, Griffith M, Griffith OL. DGIdb 2.0: mining
clinically relevant drug-gene interactions. Nucleic Acids
Research. 2016 Jan 4;44(D1):D1036-44. doi:10.1093/nar/gkv1165.
_S_e_e _A_l_s_o:
'rDGIdbResult', 'queryDGIdb', 'rDGIdbFilters'
_E_x_a_m_p_l_e_s:
queryResult <- queryDGIdb('KRAS')
plotInteractionsBySource(queryResult)
Error: processing vignette 'vignette.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `fgcolor'.
See the xcolor package documentation for explanation.
Type H <return> for immediate help.
...
! Emergency stop.
...
l.66 ...}{rgb}{0.941, 0.941, 0.941}\color{fgcolor}
\begin{kframe}
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘vignette.Rnw’
SUMMARY: processing the following file failed:
‘vignette.Rnw’
Error: Vignette re-building failed.
Execution halted