importFeatureCounts {GenomicTools.fileHandler}

Import from FeatureCounts

Description

This functions imports the output from FeatureCounts

Usage

importFeatureCounts(file, skip = 0, headerLine = 2)

Arguments

file

Character, file name

skip

Number of lines to skip from txt file

headerLine

Linenumber that contains the header information

Details

FeatureCounts produces two files, the txt that contain the expression values and then the summary that containts all the information about the mapping statistics. This function imports both and stores them in a corresponding list.

Value

A list with expValues, geneInfo and summary

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","featureCountsExample.txt", package="GenomicTools.fileHandler")
 # Import the example featureCounts file  
   fcFile <- importFeatureCounts(file=fpath)