View source: R/negative_binomial_check.R
goodness_of_fit_DESeq2 | R Documentation |
This function calculates goodness-of-fit pvalues for all genes by looking at how the NB model by DESeq2 fit the data
goodness_of_fit_DESeq2(se, count_matrix, condition, batch)
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 |
a matrix of pvalues where each row is a gene and each column is a level within the condition of interest
# 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
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