getEISAcounts-getEISAcounts: getEISAcounts

In emarmolsanchez/EISAcompR: EISAcompR: a comprehensive and user-friendly pipeline for performing Exon/Intron Split Analysis (EISA) using RNA-Seq data

getEISAcounts

Description

This function allows users to quantify the level of expression of their aligned reads by making use of custom-created exonic/intronic GTF annotation files. The featureCounts built-in function from Rsubread package is used for such purpose. Users may optionally decide to use any other preferred quantification pipeline provided the use of exonic/intronic GTF annotation as a reference.

Usage

getEISAcounts(files, annotFile, strandness, nthreads, PairedEnd = TRUE)

Arguments

files	PATH to input BAM/SAM files containing read mapping results.
annotFile	PATH to exonic/intronic GTF annotation file.
strandness	Strandness. Character. You have to select one out "unstranded","stranded_forward","stranded_reversed".
nthreads	Number of available threads for parallel computation.
PairedEnd	Boolean specifying if input sequencing data is of type Paired-end (TRUE/FALSE).

Value

results. It will create a raw count matrix stored at counts object with quantification estimates of each mapped read to the corresponding exonic/intronic regions and gene assignment.

Author(s)

Emilio Mármol Sánchez

Examples

{
## Not run: 
exon_counts <- getEISAcounts(files=vector_of_input_BAM/SAM, annotFile="PATH_to_exon_GTF",
strandness="unstranded", nthreads=4, PairedEnd=TRUE)
intron_counts <- getEISAcounts(files=vector_of_input_BAM/SAM, annotFile="PATH_to_intron_GTF",
strandness="unstranded", nthreads=4, PairedEnd=TRUE)

## End(Not run)

}

emarmolsanchez/EISAcompR documentation built on May 22, 2024, 2:07 a.m.