DESeq_large_analysis: This function calculated the goodness of fit of DESeq2 for...

In compbiomed/BatchQC: Batch Effects Quality Control Software

This function calculated the goodness of fit of DESeq2 for larger sample sizes (intended for more than 20 samples).

Description

This function calculated the goodness of fit of DESeq2 for larger sample sizes (intended for more than 20 samples).

Usage

DESeq_large_analysis(
  count_matrix,
  condition,
  other_variables,
  conditions_df,
  formula_for_DESeq,
  num_samples,
  sampled
)

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
num_samples	total number of samples to analyze
sampled	the down sampled matrix

Value

a list containing the string recommendation

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