convert_salmon: 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 (Salmon)

Description

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

Usage

convert_salmon(
  count_files = NULL,
  samples = NULL,
  indir = NULL,
  outprefix = NULL,
  txgene_fn = "",
  gene2symbol = "",
  workers = detectCores(),
  ...
)

Arguments

count_files	Character vector for salmon output count files
samples	If count_files is NULL, samples was used to set the value with indir
indir	Input salmon counts dir
outprefix	Output prefix
txgene_fn	Two columns file contains TXNAME (e.g. ENST00000373020.9) and GENEID (ENSG00000000003.15)
gene2symbol	Two columns file contains GENEID (e.g. ENSG00000000003.15) and SYMBOL (TSPAN6)
workers	Number of thread for DESeq2 process
...	countsFromAbundance ("no", "scaledTPM", "lengthScaledTPM", "dtuScaledTPM") and ignoreAfterBar (TRUE or FALSE). Default is lengthScaledTPM and TRUE

Examples

## Not run: 
  gene2symbol <- fread('~/env/genome/gencode/hg38/v34/tximport.geneid2symbol',
    header = T, data.table = FALSE)
  txgene_fn <- "~/env/genome/gencode/hg38/v34/tximport.genes"
  tx2gene <- fread(txgene_fn)

  samples <- readLines("samples")
  sampledata <- data.frame(sampleName = samples, condition = rep("disease", length(samples)))
  salmon_dir <- "../salmon/output/salmonGTF/"
  salmon_files <- file.path(salmon_dir, samples, "quant.sf")
  convert_salmon(salmon_files,
    outprefix = "salmon/aml",
    txgene_fn = txgene_fn,
    gene2symbol = gene2symbol
  )

## End(Not run)

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