TransformCount: Filter and normalize a count matrix This wrapper function...

In WubingZhang/rMAUPS: Model-Based Analysis of Ubiquitin-Proteome System Based Protein Degradation.

Filter and normalize a count matrix This wrapper function combines filtering out genes with low reads in a number of samples with normalization.

Description

Filter and normalize a count matrix This wrapper function combines filtering out genes with low reads in a number of samples with normalization.

Usage

TransformCount(
  m,
  method = c("TPM", "voom", "vst", "rlog")[1],
  idType = "Ensembl",
  org = "hsa"
)

Arguments

m	raw count matrix (genes are rows, columns are samples)
method	the normalization method, one of "none", "TPM", "voom", "vst", "rlog".
idType	same as in 'Count2TPM', only required when method = "TPM".
org	same as in 'Count2TPM', only required when method = "TPM".

Value

filtered and normalized count matrix

Author(s)

Wubing Zhang

WubingZhang/rMAUPS documentation built on March 21, 2022, 8:48 p.m.