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Test for differences in log2(Fold Change) ECDFs between two gene lists using the stats package

Source: R/ecdf_stat_test.R
ecdf_stat_test.Rd

This function uses the stats package to test the ECDF of log2(Fold Changes) between two groups based on DESeq2 analysis.

The inputs of this function are a differential expression results data.frame and two sets of gene IDs called gene.list1 and gene.list2. The functions will look for a column called log2FoldChange in the dataframe.

Usage

ecdf_stat_test(
  res,
  gene.list1,
  gene.list2,
  stats.test = c("KS", "Wilcoxen"),
  alternative = "greater",
  l2fc.col = "log2FoldChange"
)

Arguments

res

Input results file data frame

gene.list1

Gene list 1: Usually null distribution

gene.list2

Gene list 2: Target set of genes

stats.test

Stats test to use. Options: KS or Wilcoxen

alternative

The alternative hypothesis to test. Options: greater, less, two.sided

l2fc.col

The name of the column containing log2FoldChange values. Based on DESEQ2 names as default.

Value

A vector containing the dstat and pvalue

Examples

if (FALSE) { # interactive()
library(dplyr)

guide.seq = "UUAUAGAGCAAGAACACUGUUUU"

anno.db = load_species_anno_db("human")

features = get_feature_seqs(anno.db$tx.db, anno.db$dna)

# Load test data
get_example_data("sirna")

sirna.data = load_example_data("sirna")

res <- sirna.data$Schlegel_2022_Ttr_D1_30mkg

# Filter DESeq2 results for SeedMatchR
res = filter_deseq(res, fdr.cutoff=1, fc.cutoff=0, rm.na.log2fc = TRUE)

res = SeedMatchR(res, anno.db$gtf, features$seqs, guide.seq, "mer7m8")

# Gene set 1
mer7m8.list = res$gene_id[res$mer7m8 >= 1]

# Gene set 2
background.list = res$gene_id[!(res$mer7m8 %in% mer7m8.list)]

ecdf.res = ecdf_stat_test(res, mer7m8.list, background.list)
}