View source: R/ecdf_stat_test.R
ecdf_stat_test | R Documentation |
stats
packageThis 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.
ecdf_stat_test(
res,
gene.list1,
gene.list2,
stats.test = "KS",
alternative = "greater"
)
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 |
A vector containing the dstat and pvalue
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)
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