permuted_DESeq: This function performs DESeq on the permuted dataset adjusted...

In compbiomed/BatchQC: Batch Effects Quality Control Software

This function performs DESeq on the permuted dataset adjusted pvalues.

Description

This function performs DESeq on the permuted dataset adjusted pvalues.

Usage

permuted_DESeq(
  count_matrix,
  condition,
  other_variables,
  conditions_df,
  formula_for_DESeq
)

Arguments

count_matrix	matrix containing the data to be analyzed
condition	a vector containing a factor of the condition of interest (typically batch)
other_variables	a vector of strings of other variables of interest
conditions_df	data frame containing information for the other variables of interest (columns in order of the other_variables vector)
formula_for_DESeq	the stat formula to be used in the DESeq analysis

Value

a DESeq2 object

compbiomed/BatchQC documentation built on Feb. 24, 2025, 10:52 a.m.