GENEXP_CDS | R Documentation |
Map reads to CDS regions and calculate TPM for each gene.
GENEXP_CDS(CDSbygene, flS, Strandtype="NONE")
CDSbygene |
a genomic ranges of CDS regions for each coding gene |
flS |
bamfile lists containing the file and path of bam files |
Strandtype |
strand type of the bam file; "forward" is forwand sequencing, "invert" is reverse sequencing and "NONE" is non-strand specific, Default is "NONE". |
The function GENEXP_CDS()
return a dataframe containing reads count, TPM for each gene
Ruijia Wang
## count reads mapped to CDS regions and calculate TPM for each gene
## using forward sequencing
library("TBX20BamSubset")
library("Rsamtools")
library("GenomicAlignments")
library("GenomicFeatures")
library("org.Mm.eg.db")
flsall = getBamFileList()
extpath = system.file("extdata", "mm9.chr19.refGene.R.DB", package="APAlyzer")
txdb = loadDb(extpath, packageName='GenomicFeatures')
IDDB = org.Mm.eg.db
CDSdbraw = REFCDS(txdb,IDDB)
DFGENEraw = GENEXP_CDS(CDSdbraw, flsall, Strandtype="forward")
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