getrnamat: Combine count matrix for individual samples

In rosedu1/deconvSeq: Cell Type Deconvolution for RNA Sequencing and Bisulfite Sequencing

Description

Takes count matrix for individual samples (e.g. output of HTSeq output). Format: first column is Ensembl gene id, second column is count, no header. Removes genes with all 0 reads and rows that are not Ensembl gene IDs. Output is a count matrix where rows are genes and columns are samples. Sample input files: sample_genecounts1.txt, sample_genecounts2.txt

Usage

getrnamat(filnames, sample.id)

Arguments

filnames	filenames of individual samples
sample.id	sample IDs

Value

count matrix with genes in rows. First column is gene name and

Examples

file1 = system.file("extdata","sample1_genecounts.txt", package="deconvSeq")
file2 = system.file("extdata","sample2_genecounts.txt", package="deconvSeq")
countmat = getrnamat(filnames=c(file1,file2),sample.id=c("sample1","sample2"))

rosedu1/deconvSeq documentation built on Aug. 19, 2020, 7:10 p.m.