deseq2normalizedExpr: To output normalized results to files named by given...

In Tong-Chen/ImageGP: For ImageGP cloud platform (https://www.bic.ac.cn/BIC)

To output normalized results to files named by given "output_prefix", and also return a list containing normalized counts for downstream analysis.

Description

To output normalized results to files named by given "output_prefix", and also return a list containing normalized counts for downstream analysis.

Usage

deseq2normalizedExpr(
  dds,
  output_prefix = "ehbio",
  rlog = T,
  vst = F,
  savemat = T,
  design = NULL
)

Arguments

dds	salmon2deseq or readscount2deseq or DESeq generated dataset.
output_prefix	A string, will be used as output file name prefix.
rlog	Get "rlog" transformed value for downstream correlation like analysis.
vst	Get "vst" transformed value for downstream correlation like analysis. Normally faster than "rlog".
savemat	Save normalized and rlog/vst matrix to file. Default T. The file would be named like output_prefix.DESeq2.normalized.xls, output_prefix.DESeq2.normalized.rlog.xls.

Value

A list containing normalized expression values and/or rlog, vst transformed normalized expression values.

Examples

nomrexpr <- deseq2normalizedExpr(dds)

Tong-Chen/ImageGP documentation built on April 14, 2025, 12:54 p.m.