getCohortExonExpressionData: Generate a data frame of cohort exon expression data

In jefferys/FusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description

Load all the exon expression files for a cohort of samples and build a single data frame with exon information from a geneModels data frame and one column of expression information per sample in the cohort. This takes a while, so progress by sample is reported by default.

Usage

getCohortExonExpressionData(geneModels, cohortFiles, progress = TRUE,
  type = "rpkm")

Arguments

geneModels	A data frame describing the exon structure of the genes (gene models). See loadGafModels. This must correspond to the exon expression file exon names.
cohortFiles	A data frame describing the samples and their exon expression files. See loadCohortDefinition. All files must exist, a simple check is all( file.exists( cohortFiles$exonExpressionFile)).
progress	By default shows a progress bar. Set this to FALSE if don't want this (e.g. if you are logging output when running this in a batch job).
type	The type of expression being used. This is the name of the column from the exon expression files to use. By default uses the column named "rpkm". See loadExonExpressionFile

Value

Returns a data frame that concatenates the columns from the gene models data frame with one column from each sample in the cohort data frame.

jefferys/FusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.