count_transcripts: determine how many transcripts are annotated in a FASTA or...

Description Usage Arguments Value Examples

View source: R/count_transcripts.R

Description

determine how many transcripts are annotated in a FASTA or GTF file

Usage

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count_transcripts(f, fasta = TRUE, identifier = "transcript_id",
  attrsep = "; ")

Arguments

f

character, path to a file in FASTA or GTF format

fasta

TRUE if f is a fasta file; FALSE if f is a GTF file

identifier

if f is a GTF file, how are transcripts identified in the attributes field (9th column) of the file? Default transcript_id.

attrsep

if f is a GTF file, how are attributes separated in the attributes field (9th column) of the file? Default "; ".

Value

Number of transcripts annotated in f

Examples

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fastapath = system.file("extdata", "chr22.fa", package="polyester")
count_transcripts(fastapath) #918

mikelove/polyesterAlpineMs documentation built on May 22, 2019, 10:52 p.m.