bam2sig {rnaSeqMap} | R Documentation |
Reads BAM files according to annotation and produces output table processed with DESeq negative binomial test.
bam2sig(annotlib, covdesc="covdesc", species=NULL, level="gene")
annotlib |
Character table or data frame with colums: chr, start, end, strand, name |
covdesc |
Name of the file that includes BAM files (experiment description file) |
species |
Species name - needed for .chr.convert function - to match BAM and annotation chromosome names |
level |
The level of annotation for calculating the counts: gene, transcript of exon |
Output table with significant expression results, as from DESeq
Michal Okoniewski, Anna Lesniewska
if (1==0) { all.g <- all.genes(as.vector=F) ss <- sample(1:20000, 10) genes <- as.data.frame(all.g[ss,]) deseqRes <- bam2sig("cassava.db") deseqRes[1:10,] }