stringtie_quantify: Quantify expression in TPM with StringTie

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

Quantify expression in TPM with StringTie

Description

Quantify expression in TPM with StringTie

Usage

stringtie_quantify(
  sample_info = NULL,
  qc_table = NULL,
  mappingdir = "results/04_read_mapping",
  gff_path = NULL,
  stringtiedir = "results/05_quantification/stringtie",
  threads = 1
)

Arguments

sample_info	Data frame of sample metadata created with the functions create_sample_info and infer_strandedness. The function infer_strandedness adds a column named "Orientation" with library strandedness information, which is mandatory.
qc_table	Data frame of fastp summary statistics as returned by summary_stats_fastp().
mappingdir	Directory where .bam files are stored.
gff_path	Path to GFF/GTF file with annotations.
stringtiedir	Directory where StringTie output files will be stored.
threads	Number of threads to use. Default: 1.

Value

A 2-column data frame with samples in the first column and status in the second column, with "OK" if expression in TPM was obtained, 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_quantify(sample_info, qc_table, mappingdir, 
                            gff_path, stringtiedir)
}

almeidasilvaf/gead documentation built on April 26, 2023, 3:47 p.m.