readBiokitGctFile: Read GCT files from Biokit output directory

In bedapub/ribiosNGS: Utilities for next-generation sequencing data analysis in ribios

Read GCT files from Biokit output directory

Description

Read GCT files from Biokit output directory

Usage

readBiokitGctFile(
  dir,
  anno = c("refseq", "ensembl"),
  type = c("count", "tpm", "count_collapsed", "tpm_collapsed", "log2tpm")
)

Arguments

dir	Biokit output directory
anno	Annotation type, either refseq or ensembl is supported
type	GCT file type, count, tpm, count_collapsed, tpm_collapsed, and log2tpm are supported.

Value

A numeric matrix with the attribute desc encoding the values in the description column of the GCT format.

The function depends on gct (in case anno="refseq") or gct-ens (in case anno="ensembl") sub-directory in the biokit output directory.

Examples

##... (TODO: add a mock output directory in testdata)

bedapub/ribiosNGS documentation built on Feb. 10, 2025, 12:34 a.m.