count_transcripts {polyester}R Documentation

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

Description

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

Usage

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

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


[Package polyester version 1.30.0 Index]