Description Usage Arguments Value Examples
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
1 | getrnamat(filnames, sample.id)
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filnames |
filenames of individual samples |
sample.id |
sample IDs |
count matrix with genes in rows. First column is gene name and
1 2 3 | 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"))
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