stringtie2se: Create a SummarizedExperiment object from StringTie output

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

Create a SummarizedExperiment object from StringTie output

Description

Create a SummarizedExperiment object from StringTie output

Usage

stringtie2se(
  sample_info = NULL,
  stringtiedir = "results/05_quantification/stringtie",
  level = "gene",
  tx2gene = NULL,
  countsFromAbundance = "lengthScaledTPM"
)

Arguments

sample_info	Data frame of sample metadata created with the functions create_sample_info
stringtiedir	Directory where StringTie output files are stored.
level	Character indicating to which level expression must be quantified in the SE object. One of "gene" (default), "transcript", or "both". For "both", the SE object will have two assays named "transcript" and "gene".
tx2gene	Data frame of correspondence between genes and transcripts, with gene IDs in the first column and transcript IDs in the second column. Only required if level = 'gene' or 'both'.
countsFromAbundance	Exactly as in tximport::tximport, whether ot not to generate estimated counts using abundance estimates. One of "lengthScaledTPM" (default), "scaledTPM", "no", or "dtuScaledTPM". See ?tximport for details.

Value

A SummarizedExperiment object with gene/transcript expression levels and sample metadata.

Examples

data(sample_info)
qc_table <- summary_stats_fastp(system.file("extdata", package = "bears"))
data(tx2gene)
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)
    se_gene <- stringtie2se(sample_info, stringtiedir, tx2gene = tx2gene)
}

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