readGeneExp {DEGseq} | R Documentation

## 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,]

[Package DEGseq version 1.40.0 Index]