xseq: Assessing Functional Impact on Gene Expression of Mutations in Cancer

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.

Author
Jiarui Ding, Sohrab Shah
Date of publication
2015-09-11 08:04:31
Maintainer
Jiarui Ding <jiaruid@cs.ubc.ca>
License
GPL (>= 2)
Version
0.2.1

View on CRAN

Man pages

cna.call
TCGA AML SNP6.0 GISTIC copy number alteration calls
cna.logr
TCGA AML SNP6.0 copy number alteration data
ConvertXseqOutput
Convert xseq output to a data.frame
EstimateExpression
A mixture modelling approach to estiamte whether a gene is...
expr
TCGA AML SNP6.0 gene expression data
FilterNetwork
Filter network
GetExpressionDistribution
Get the conditional distributions for a set of genes
ImputeKnn
Impute missing values (NAs) using K-nearest neighbour...
InferXseqPosterior
Learn xseq parameters given an initialized model
InitXseqModel
The datastructure to store the xseq models
LearnXseqParameter
Learn xseq parameters given an initialized model
mut
TCGA AML somatic mutation data
net
A networks containing gene associations
NormExpr
Remove the cis-effects of copy number alterations on gene...
PlotRegulationHeatmap
Heatmap showing the connected genes' dysregulation...
QuantileNorm
Quantile normalize a matrix
SetXseqPrior
Set model paramerter priors

Files in this package

xseq
xseq/inst
xseq/inst/doc
xseq/inst/doc/xseq-package.R
xseq/inst/doc/xseq-package.Rmd
xseq/inst/doc/xseq-package.pdf
xseq/src
xseq/src/mix_gauss_prob.c
xseq/src/xseq.h
xseq/src/register.c
xseq/src/log_sum_exp.c
xseq/NAMESPACE
xseq/data
xseq/data/expr.rda
xseq/data/mut.rda
xseq/data/cna.call.rda
xseq/data/net.rda
xseq/data/cna.logr.rda
xseq/R
xseq/R/mix_model_help.R
xseq/R/xseq_init_expr_dis.R
xseq/R/mix_student_fit_em.R
xseq/R/xseq_plot.R
xseq/R/data.R
xseq/R/mix_gauss_fit_em.R
xseq/R/mix_model_plot.R
xseq/R/mix_model_set_prior.R
xseq/R/xseq_expr_dis.R
xseq/R/mix_model_init.R
xseq/R/util.R
xseq/R/heatmap.3.R
xseq/R/xseq_inference_learning.R
xseq/R/zzz.R
xseq/vignettes
xseq/vignettes/xseq-package.html
xseq/vignettes/xseq-package.Rmd
xseq/MD5
xseq/build
xseq/build/vignette.rds
xseq/DESCRIPTION
xseq/man
xseq/man/mut.Rd
xseq/man/InferXseqPosterior.Rd
xseq/man/cna.logr.Rd
xseq/man/FilterNetwork.Rd
xseq/man/ImputeKnn.Rd
xseq/man/expr.Rd
xseq/man/GetExpressionDistribution.Rd
xseq/man/NormExpr.Rd
xseq/man/PlotRegulationHeatmap.Rd
xseq/man/LearnXseqParameter.Rd
xseq/man/InitXseqModel.Rd
xseq/man/QuantileNorm.Rd
xseq/man/ConvertXseqOutput.Rd
xseq/man/SetXseqPrior.Rd
xseq/man/cna.call.Rd
xseq/man/net.Rd
xseq/man/EstimateExpression.Rd