InitXseqModel: The datastructure to store the xseq models

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

Description

The datastructure to store the xseq models

Usage

InitXseqModel(mut, expr, net, expr.dis, prior, cpd, gene, p.h, weight,
  cis = FALSE, debug = FALSE)

Arguments

mut	A data.frame of mutations. The data.frame should have three columns of characters: sample, hgnc_symbol, and variant_type. The variant_type column cat be either "HOMD", "HLAMP", "MISSENSE", "NONSENSE", "FRAMESHIFT", "INFRAME", "SPLICE", "NONSTOP", "STARTGAINED", "SYNONYMOUS", "OTHER", "FUSION", "COMPLEX".
expr	A matrix of gene expression values where each row corresponds to a patient and each column is a gene
net	A list of gene interaction networks
expr.dis	The fitted gene expression distributions, output from GetExpressionDistribution
prior	The prior for xseq, output from SetXseqPrior
cpd	A list of conditional probability tables for xseq, output from SetXseqPrior
gene	A character vector of gene names, default to all the genes with mutations
p.h	The down-regulation probability list of each gene connected to a mutated gene, typically from running LearnXseqParameter on a discovery dataset
weight	The weight list of each gene connected to a mutated gene, typically from running LearnXseqParameter on a discovery dataset
cis	Logical, cis or trans analysis
debug	Logical, whether to output debug information

Value

A xseq model

xseq documentation built on May 1, 2019, 9:47 p.m.