makeEISAgtfs-makeEISAgtfs: makeEISAgtfs

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

makeEISAgtfs

Description

This is the first function of EISACompR. makeEISAgtfs aims to build custom annotation files in GTF format for late reads quantification spanning either exonic or intronic genomic ranges. Reference GTF annotation for your species of interest is needed in order to generate the corresponding exonic/intronic regions for running EISA analysis.

Usage

makeEISAgtfs(annotFile, boundaryFix = 10, show_message = TRUE)

Arguments

annotFile	PATH to reference GTF annotation file.
boundaryFix	Exon junction boundary correction threshold (10 bp by default).
show_message	(logical) if TRUE the proccess history is printed. Default TRUE.
path_temp_files	Home is the default "~/". This argument indicates the path were the temp_dir with exons, introns info should be created.

Value

results. It returns a EIsacompR object with the exons and introns information

Author(s)

Emilio Mármol Sánchez

Examples

{
## Not run: 
GTFS<-makeEISAgtfs(annotFile="path_to_ann_file")

## End(Not run)

}

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