SeedMatchR (version 1.1.1)

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

Description

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 DESeq2 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 = "KS",
  alternative = "greater"
)

Value

A vector containing the dstat and pvalue

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

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)
}