DEGseq (version 1.26.0)

readGeneExp: readGeneExp: read gene expression values to a matrix

Description

This method is used to read gene expression values from a file to a matrix in R workspace. So that the matrix can be used as input of other packages, such as edgeR. The input of the method is a file that contains gene expression values.

Usage

readGeneExp(file, geneCol=1, valCol=2, label = NULL, header=TRUE, sep="")

Arguments

file

file containing gene expression values.

geneCol

gene id column in file.

valCol

expression value columns to be read in the file.

label

label for the columns.

header

a logical value indicating whether the file contains the names of the variables as its first line. See ?read.table.

sep

the field separator character. If sep = "" (the default for read.table) the separator is white space, that is one or more spaces, tabs, newlines or carriage returns. See ?read.table.

See Also

getGeneExp, GeneExpExample1000, GeneExpExample5000.

Examples

## If the data files are collected in a zip archive, the following
  ## commands will first extract them to the temporary directory.

  geneExpFile <- system.file("extdata", "GeneExpExample1000.txt", package="DEGseq")
  exp <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c(7,9,12,15,18,8,10,11,13,16))
  exp[30:35,]