align_free_quan: Alignment-free expression quantification with Salmon at gene...

View source: R/align_free_quan.R

align_free_quanR Documentation

Alignment-free expression quantification with Salmon at gene and transcript levels.

Description

Alignment-free expression quantification with Salmon at gene and transcript levels.

Usage

align_free_quan(
  pair,
  genome,
  transcript,
  annotation,
  threads = 4,
  salmon_index_add = NULL,
  salmon_quan_add = NULL
)

Arguments

pair

'single' for single-end (SE) or 'paired' for paired-end (PE) reads.

genome

the reference genome.

transcript

the reference transcript

annotation

the annotation file.

threads

the number of threads to be used. Default is 4.

salmon_index_add

additional parameters to customize salmon index command. Default is NULL.

salmon_quan_add

additional parameters to customize salmon quan command. Default is NULL.

Value

None

Examples


align_free_quan(
pair = 'paired', 'test_Homo_sapiens.fna', 
'test_transcript_Homo_sapiens.fna','test_Homo_sapiens.gff'
)




sunshanwen/BP4RNAseq documentation built on March 28, 2022, 5:35 p.m.