goodness_of_fit_DESeq2: This function calculates goodness-of-fit pvalues for all...

In compbiomed/BatchQC: Batch Effects Quality Control Software

This function calculates goodness-of-fit pvalues for all genes by looking at how the NB model by DESeq2 fit the data

Description

This function calculates goodness-of-fit pvalues for all genes by looking at how the NB model by DESeq2 fit the data

Usage

goodness_of_fit_DESeq2(se, count_matrix, condition, batch)

Arguments

se	the se object where all the data is contained
count_matrix	name of the assay with gene expression matrix (in counts)
condition	name of the se colData with the condition status
batch	name of the se colData containing batch information

Value

a matrix of pvalues where each row is a gene and each column is a level within the condition of interest

Examples

# example code
library(scran)
se <- mockSCE(ncells = 20)
nb_results <- goodness_of_fit_DESeq2(se = se, count_matrix = "counts",
  condition = "Treatment", batch = "Mutation_Status")
nb_results

compbiomed/BatchQC documentation built on Aug. 1, 2024, 8:10 p.m.