prepare_count_data: Prepare count data

In szymczak-lab/harmonizeGeneExprData: Harmonization of gene expression data from GEO and ArrayExpress

Prepare count data

Description

Remove genes with only zero counts across samples and perform voom transformation (as implemented in voom)

Usage

prepare_count_data(counts)

Arguments

counts

[data.frame or matrix] raw counts with genes in rows and samples in columns

Value

[list] assays (counts, voom and voom.weights) to be used in make_se_object

Examples

# define temporary directory for storing file from recount
temp.dir = tempdir()

# get counts from recount
library(recount)
download_study(
  project = "SRP057087",
  type = "counts-gene",
  outdir = temp.dir)
counts = read.table(
  file.path(temp.dir, "counts_gene.tsv.gz"),
  header = TRUE,
  row.names = 29)

assays = prepare_count_data(counts)

szymczak-lab/harmonizeGeneExprData documentation built on Dec. 1, 2022, 9:07 p.m.