nb_proportion: This function determines the proportion of p-values below a...

In compbiomed/BatchQC: Batch Effects Quality Control Software

This function determines the proportion of p-values below a specific value and compares to the previously determined threshold of 0.42 for extreme low values.

Description

This function determines the proportion of p-values below a specific value and compares to the previously determined threshold of 0.42 for extreme low values.

Usage

nb_proportion(p_val_table, low_pval = 0.01, threshold = 0.42)

Arguments

p_val_table	table of p-values from the nb test
low_pval	value of the p-value cut off to use in proportion
threshold	the value to compare the p-values to

Value

a statement about whether DESeq2 is appropriate to use for analysis

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_proportion(nb_results, low_pval = 0.01, threshold = 0.42)

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