readGeneExp {DEGseq} | R Documentation |
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.
readGeneExp(file, geneCol=1, valCol=2, label = NULL, header=TRUE, sep="")
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 |
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 |
getGeneExp
,
GeneExpExample1000
,
GeneExpExample5000
.
## 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,]