Assessing Functional Impact on Gene Expression of Mutations in Cancer


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Documentation for package ‘xseq’ version 0.2.1

Help 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 expressed in a study given RNA-seq gene expression data
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 averaging
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 expression
PlotRegulationHeatmap Heatmap showing the connected genes' dysregulation probabilities
QuantileNorm Quantile normalize a matrix
SetXseqPrior Set model paramerter priors