GENEXP_CDS {APAlyzer} | R Documentation

## GENEXP_CDS, count reads mapped to CDS regions and calculate TPM for coding gene

### Description

Map reads to CDS regions and calculate TPM for each gene.

### Usage

        GENEXP_CDS(CDSbygene, flS, Strandtype="NONE")

### Arguments

`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".

### Value

The function `GENEXP_CDS()` return a dataframe containing reads count, TPM for each gene

### Author(s)

Ruijia Wang

### Examples

    ## 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")

[Package APAlyzer version 1.1.2 Index]