Last data update: 2014.03.03
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xseq
Package: xseq
Title: Assessing Functional Impact on Gene Expression of Mutations in
Cancer
Version: 0.2.1
Date: 2015-08-25
Author: Jiarui Ding, Sohrab Shah
Maintainer: Jiarui Ding <jiaruid@cs.ubc.ca>
Depends: R (>= 3.1.0)
Imports: e1071 (>= 1.6-4), gptk (>= 1.08), impute (>= 1.38.1),
preprocessCore (>= 1.26.1), RColorBrewer (>= 1.1-2), sfsmisc
(>= 1.0-27)
Suggests: knitr
Description: A hierarchical Bayesian approach to assess functional impact of mutations on gene expression in cancer. Given a patient-gene matrix encoding the presence/absence of a mutation, a patient-gene expression matrix encoding continuous value expression data, and a graph structure encoding whether two genes are known to be functionally related, xseq outputs: a) the probability that a recurrently mutated gene g influences gene expression across the population of patients;
and b) the probability that an individual mutation in gene g in an individual patient m influences expression within that patient.
License: GPL (>= 2)
LazyLoad: ture
Packaged: 2015-09-10 19:21:43 UTC; jding
VignetteBuilder: knitr
LazyData: TRUE
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-09-11 08:04:31
Install log
* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'xseq' ...
** package 'xseq' successfully unpacked and MD5 sums checked
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c log_sum_exp.c -o log_sum_exp.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c mix_gauss_prob.c -o mix_gauss_prob.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c register.c -o register.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o xseq.so log_sum_exp.o mix_gauss_prob.o register.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/xseq/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'xseq'
finding HTML links ... done
ConvertXseqOutput html
EstimateExpression html
FilterNetwork html
GetExpressionDistribution html
ImputeKnn html
InferXseqPosterior html
InitXseqModel html
LearnXseqParameter html
NormExpr html
PlotRegulationHeatmap html
QuantileNorm html
SetXseqPrior html
cna.call html
cna.logr html
expr html
mut html
net html
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xseq)
Making 'packages.html' ... done
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