transform_value: Transform normalized expression matrix by vst or rlog

In goushixue/QRseq: Quickly RNA-seq Analysis Platform

Transform normalized expression matrix by vst or rlog

Description

Transform normalized expression matrix by vst or rlog

Usage

transform_value(
  object,
  blind,
  fitType,
  nsub,
  trans.method,
  batch.method = "NULL",
  batch = NULL,
  batch2 = NULL
)

Arguments

object	dds object
blind	logical, whether to blind the transformation to the experimental design.
fitType	either "parametric", "local", or "mean" for the type of fitting of dispersions to the mean intensity.
nsub	the number of genes to subset to (default 1000)
trans.method	method for transforming data, 'rlog' or 'vst'
batch.method	method for remove batch effects, 'ComBat', 'removeBatchEffect' or NULL
batch	a column name will treated as batch effector

goushixue/QRseq documentation built on July 9, 2023, 9:28 a.m.