# Assessing Functional Impact on Gene Expression of Mutations in Cancer

## Documentation for package ‘xseq’ version 0.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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