PASEXP_IPA {APAlyzer} | R Documentation

## PASEXP_IPA, calculate relative expression of IPA regions

### Description

Map reads to IPA regions and calculte relative expression of aUTR and cUTR regions.

### Usage

        PASEXP_IPA(dfIPAraw, dfLEraw, flS, Strandtype="NONE", nts=1, minMQS=0)

### Arguments

`dfIPAraw` | a dataframe containing 8 colmuns for Intronic PASs: 'PASid', 'gene_symbol', 'Chrom', 'Strand', 'Pos', 'upstreamSS', 'downstreamSS'. 'upstreamSS' means closest 5'/3' splice site to IPA, 'downstreamSS' means closest 3' splice site
`dfLEraw` | a dataframe containing 5 colmuns for 3' least exon: 'gene_symbol', 'Chrom', 'Strand', 'LEstart', 'TES'. 'LEstart' means the start position of last 3' exon.
`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".
`nts` | number of threads used for computing, parameter used by featureCounts, nthread option, Default is 1
`minMQS` | minimum mapping quality score of counted reads, parameter used by featureCounts, minMQS option, Default is 0

### Value

The function `PASEXP_IPA()` return a dataframe containning reads count, RPKM and relative expression of aUTR and cUTR for each gene

### Author(s)

Ruijia Wang

### Examples

    ## count reads mapped to IPA regions and
    ## calculte relative expression of aUTR and cUTR regions
    ## using forward sequencing
        library("TBX20BamSubset")
        library("Rsamtools")
        library("GenomicAlignments")
    	library("repmis")
        flsall = getBamFileList()
    	URL="https://github.com/RJWANGbioinfo/PAS_reference_RData/blob/master/"
    	file="mm9_REF.RData"
    	source_data(paste0(URL,file,"?raw=True"))
        IPA_OUTraw=PASEXP_IPA(dfIPA, dfLE, flsall, Strandtype="forward", nts=1)

[Package APAlyzer version 1.4.0 Index]