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Test for differences in log2(Fold Change) ECDFs between two gene lists

ecdf_stat_test.Rd

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

The inputs of this function are a DE results data.frame and two sets of gene IDs called target_list and background_list. The functions will look for a column called log2FoldChange in the data frame.

The user can choose 4 tests for comparing the ECDFs of two gene sets. Options: KS, Wilcoxen, Wass, or DTS.

When looking at siRNA off-target effects use alternative = "greater". If you are looking at effects on miRNA targets, use alternative = "lesser". If you do not know which direction of change will occur, use alternative = "two.sided".

Usage

ecdf_stat_test(
  res,
  target_list,
  background_list,
  stats_test = c("KS", "Wilcoxen", "Wass", "DTS"),
  alternative = c("greater", "two.sided", "less")
)

Arguments

res

Input results file data frame.

target_list

Target set of genes.

background_list

Set of genes that will be used as background distribution.

stats_test

Stats test to use. Options: KS, Wilcoxen, Wass, and DTS.

alternative

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

Value

A vector containing the test statistic and p-value.

Examples

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

guide.seq = "UUAUAGAGCAAGAACACUGUUUU"

anno.db = load_annotations("rnor7")

# 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_res(res, fdr.cutoff=1, fc.cutoff=0, rm.na.log2fc = TRUE)

res = SeedMatchR(res = res, gtf = anno.db$gtf, seqs = anno.db$seqs,
sequence = guide.seq, seed.name = "mer7m8", tx.id.col= FALSE)

# 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 = SeedMatchR::ecdf_stat_test(res, mer7m8.list, background.list)
}