taco_merge: Merge assembled transcripts with TACO

In almeidasilvaf/GEAtlas: Building Expression Atlas from RNA-Seq data

Merge assembled transcripts with TACO

Description

This function merges GFF files from StringTie assembly into a single GFF.

Usage

taco_merge(
  sample_info = NULL,
  stringtiedir = "results/05_quantification/stringtie",
  threads = 1
)

Arguments

sample_info	Data frame of sample metadata created with the function create_sample_info.
stringtiedir	Directory where StringTie output files will be stored.
threads	Number of threads to use. Default: 1.

Details

The GFF files for each BioSample are first merged into BioProject-level GFF files. Then, these Bioproject-level GFF files are merged into a single file that represents the whole set.

Value

A 2-column data frame with the TACO run status, with "OK" if the program merged transcripts successfully, and NA otherwise.

Examples

data(sample_info)
qc_table <- summary_stats_fastp(system.file("extdata", package = "bears"))
mappingdir <- system.file("extdata", package="bears")
gff_path <- system.file("extdata", "Homo_sapiens.GRCh37.75_subset.gtf",
                        package="bears")
stringtiedir <- tempdir()
if(stringtie_is_installed()) {
    a <- stringtie_assemble(sample_info, qc_table, mappingdir, 
                            gff_path, stringtiedir)
}
if(taco_is_installed()) {
    taco_merge(sample_info, stringtiedir)
}

almeidasilvaf/GEAtlas documentation built on April 14, 2023, 6:58 p.m.