bam2sig: bam2sig - encapsulated pipeline of finding significant...
In rnaSeqMap: rnaSeq secondary analyses

Description Usage Arguments Value Author(s) Examples

Reads BAM files according to annotation and produces output table processed with DESeq negative binomial test.

1	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,]
  }