convert_featurecounts: Function to convert RNA-Seq reads to gene expression matrix...

In clindet/clinaml: Clinical diagnosis tool for AML

Function to convert RNA-Seq reads to gene expression matrix (featureCounts)

Description

Function to convert RNA-Seq reads to gene expression matrix (featureCounts)

Usage

convert_featurecounts(
  countfiles = NULL,
  samples = NULL,
  indir = NULL,
  meanFragmentLength = NULL,
  out_raw_counts = "",
  outprefix = NULL,
  gene2symbol = "",
  workers = detectCores()
)

Arguments

samples	If count_files is NULL, samples was used to set the value with indir
indir	Input salmon counts dir
meanFragmentLength	Character vector for sequencing library length of samples (e.g. 50, 75, 150, 200)
out_raw_counts	Output path of raw counts table with extra fields
outprefix	Output prefix
gene2symbol	Two columns file contains GENEID (e.g. ENSG00000000003.15) and SYMBOL (TSPAN6)
workers	Number of thread for DESeq2 process
count_files	Character vector for salmon output count files

Examples

samples <- readLines("samples")
countfiles <- file.path("../featureCounts", paste0(samples, ".txt"))
out_raw_counts <- "featurecounts/raw_counts_584.txt"
meanFragmentLength <- rep(150, length(samples))
meanFragmentLength[366:477] <- 75
gene2symbol <- fread('~/env/genome/gencode/hg38/v34/tximport.geneid2symbol',
    header = T, data.table = FALSE)
convert_featurecounts(countfiles,
  meanFragmentLength = meanFragmentLength,
  out_raw_counts = out_raw_counts,
  outprefix = "featurecounts/aml-",
  gene2symbol = gene2symbol)

clindet/clinaml documentation built on Jan. 3, 2023, 6:13 a.m.