runFisher performs Fisher's Exact Test to determine the enrichment of
a set of genes within reference gene sets.
Arguments
- genes
A
charactervector of genes of interest.- reference
A
charactervector of reference genes.- inputSet
A
listcontaining gene set collections. If ptm isTRUE, this should be a data frame with specific columns.- ptm
Logical. IfTRUE, perform the test on post-translational modification (PTM) gene sets. Default isFALSE.
Value
A data frame with the results of the Fisher's Exact Test,
including the gene set name, the number of genes in the set, set size,
p-value, adjusted p-value, and the genes in the set.
Details
The function can operate in two modes: standard gene sets and PTM-specific gene sets. For PTM-specific gene sets, additional filtering and processing are performed.
Examples
library(SummarizedExperiment)
library(piano)
# Load multiAssayExperiment object
data("dda_example")
# Get SummarizedExperiment object
se <- dda_example[["Proteome"]]
colData(se) <- colData(dda_example)
# Preprocess the proteome assay
result <- preprocessProteome(se, normalize = TRUE)
# Call the function to perform differential expression analyis
de <- performDifferentialExp(se = result, assay = "Intensity",
method = "limma", reference = "1stCrtl", target = "EGF",
condition = "treatment")
genesList <- unique(de$resDE$Gene)
referenceList <- unique(SummarizedExperiment::rowData(result)$Gene)
genesetPath <- appDir <- system.file("shiny-app/geneset",
package = "SmartPhos")
inGMT <- loadGSC(paste0(genesetPath,"/Cancer_Hallmark.gmt"),type="gmt")
# Run the function
runFisher(genes = genesList, reference = referenceList, inputSet = inGMT)
#> Name Gene.number Set.size pval
#> 1 HALLMARK_TNFA_SIGNALING_VIA_NFKB 1 1 1
#> 2 HALLMARK_HYPOXIA 3 3 1
#> 3 HALLMARK_MITOTIC_SPINDLE 3 3 1
#> 4 HALLMARK_IL6_JAK_STAT3_SIGNALING 1 1 1
#> 5 HALLMARK_DNA_REPAIR 2 2 1
#> 6 HALLMARK_G2M_CHECKPOINT 1 1 1
#> 7 HALLMARK_APOPTOSIS 2 2 1
#> 8 HALLMARK_ESTROGEN_RESPONSE_EARLY 5 5 1
#> 9 HALLMARK_ESTROGEN_RESPONSE_LATE 2 2 1
#> 10 HALLMARK_ANDROGEN_RESPONSE 2 2 1
#> 11 HALLMARK_MYOGENESIS 3 3 1
#> 12 HALLMARK_PROTEIN_SECRETION 2 2 1
#> 13 HALLMARK_APICAL_JUNCTION 1 1 1
#> 14 HALLMARK_COMPLEMENT 2 2 1
#> 15 HALLMARK_UNFOLDED_PROTEIN_RESPONSE 1 1 1
#> 16 HALLMARK_MTORC1_SIGNALING 4 4 1
#> 17 HALLMARK_E2F_TARGETS 2 2 1
#> 18 HALLMARK_MYC_TARGETS_V1 2 2 1
#> 19 HALLMARK_MYC_TARGETS_V2 2 2 1
#> 20 HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION 2 2 1
#> 21 HALLMARK_XENOBIOTIC_METABOLISM 1 1 1
#> 22 HALLMARK_OXIDATIVE_PHOSPHORYLATION 2 2 1
#> 23 HALLMARK_GLYCOLYSIS 4 4 1
#> 24 HALLMARK_REACTIVE_OXIGEN_SPECIES_PATHWAY 2 2 1
#> 25 HALLMARK_UV_RESPONSE_DN 1 1 1
#> 26 HALLMARK_HEME_METABOLISM 2 2 1
#> 27 HALLMARK_IL2_STAT5_SIGNALING 1 1 1
#> 28 HALLMARK_BILE_ACID_METABOLISM 1 1 1
#> 29 HALLMARK_PEROXISOME 2 2 1
#> 30 HALLMARK_KRAS_SIGNALING_DN 2 2 1
#> Genes padj
#> 1 CYR61 1
#> 2 CYR61, I.... 1
#> 3 ARHGAP10.... 1
#> 4 HAX1 1
#> 5 SDCBP, S.... 1
#> 6 DDX39A 1
#> 7 DFFA, DNM1L 1
#> 8 KRT19, K.... 1
#> 9 KRT19, S.... 1
#> 10 KRT19, KRT8 1
#> 11 BIN1, MY.... 1
#> 12 AP3B1, DNM1L 1
#> 13 WASL 1
#> 14 ATOX1, KIF2A 1
#> 15 NOP56 1
#> 16 PLOD2, P.... 1
#> 17 NOP56, D.... 1
#> 18 NOP56, P.... 1
#> 19 PES1, NOP56 1
#> 20 CYR61, PLOD2 1
#> 21 PGRMC1 1
#> 22 PDHX, NDUFS8 1
#> 23 PLOD2, K.... 1
#> 24 PDLIM1, .... 1
#> 25 CYR61 1
#> 26 SDCBP, PSMD9 1
#> 27 MYO1C 1
#> 28 SULT2B1 1
#> 29 NUDT19, .... 1
#> 30 KRT15, KRT5 1