loadExonExpressionFile: Load a TCGA exon expression data file as a data frame

In jefferys/fusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description

Loads an RNA exon expression data file as generated for the TCGA, returning its contents as a data frame. The input file has four tab-delimited columns, no header. The first column in the file describes the exon as <chr>:<start>-<end><strand>, the next three give count, coverage, and rpkm values.

Usage

loadExonExpressionFile(path)

Arguments

path	The path to the exon expression data file to load

Value

A data frame with the following columns from the exon expression file:

chr	The exon's chromosome
start	The genomic start coordinate for the exon
end	The genomic end coordinate for the exon
strand	The strand the chromosome is on, one of + | - | *
count	One of the exon expression level columns
coverage	One of the exon expression level columns
rpkm	One of the exon expression level columns

Errors

The following fatal errors can occur:

No such file: path

The exon expression file named can not be found. Case, spelling permission and wrong working dir for relative paths are all common errors.

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