selModel: Select transcript models

In pram: Pooling RNA-seq datasets for assembling transcript models

Description

Select transcript models

Usage

selModel(fin_gtf, fout_gtf, min_n_exon = 2, min_tr_len = 200,
    info_keys = c("transcript_id"))

Arguments

fin_gtf	Character of an input GTF file that contains transcript models. Required to have 'transcript_id' in the attribute column (column 9)
fout_gtf	Character of an output GTF file that contains selected transcript models
min_n_exon	Minimium number of exons a transcript model required to have Default: 2
min_tr_len	Minimium length (bp) of exon(s) and intron(s) a transcript model required to have Default: 200
info_keys	A vector of characters defining the attributes in input GTF file's column 9 to be saved in the output GTF file. 'transcript_id' will always be saved. Default: c( 'transcript_id' )

Value

None

Examples

fin_gtf = system.file('extdata/gtf/selModel_in.gtf', package='pram')

fout_gtf = tempfile(fileext='.gtf')


selModel(fin_gtf, fout_gtf)

pram documentation built on Nov. 8, 2020, 11:08 p.m.