prepareInputs: NMDer workflow: Import files

In fursham-h/ponder:

Description

Imports mandatory files for NMDer analysis

Usage

prepareInputs(queryFile, refFile, fasta, user_query_format, user_ref_format)

Arguments

queryFile	Path to query GTF/GFF3 transcript annotation file
refFile	Path to ref GTF/GFF3 transcript annotation file
fasta	BSGenome object (preferred) or path to fasta file
user_query_format	optional argument to specify the query annotation format ('gtf','gff3')
user_ref_format	optional argument to specify the refFileerence annotation format ('gtf','gff3')

Value

A list containing (1) GRanges object for query, (2) GRanges object for ref annotation, and (3) DNAstring containing genome sequence

fursham-h/ponder documentation built on Dec. 27, 2019, 12:15 a.m.