EnrichAB {MAGeCKFlute} | R Documentation |
Do enrichment analysis for selected genes, in which positive selection and negative selection are termed as GroupA and GroupB
EnrichAB(data, pvalue = 0.25, enrich_method = "ORT", organism = "hsa", pathway_limit = c(3, 50), adjust = "BH", filename = NULL, out.dir = ".", gsea = FALSE, width = 6.5, height = 4, ...)
data |
A data frame containing columns "diff", with rownames of Entrez IDs. |
pvalue |
Pvalue cutoff. |
enrich_method |
One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test). |
organism |
"hsa" or "mmu". |
pathway_limit |
A two-length vector (default: c(3, 50)), specifying the min and max size of pathways for enrichent analysis. |
adjust |
One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", and "none". |
filename |
Suffix of output file name. |
out.dir |
Path to save plot to (combined with filename). |
gsea |
Boolean, specifying if do GSEA for GroupA and GroupB genes. Default gsea = FALSE. |
width |
As in ggsave. |
height |
As in ggsave. |
... |
Other available parameters in ggsave. |
A list containing enrichment results for each group genes. This list contains items four
items, keggA
, keggB
, goA
, goB
. Four items are all list object, containing
subitems of gridPlot
and enrichRes
. gridPlot
is a ggplot object, and
enrichRes
is a enrichResult instance
Binbin Wang
data(mle.gene_summary) # Read beta score from gene summary table in MAGeCK MLE results dd = ReadBeta(mle.gene_summary, organism="hsa") data=ScatterView(dd, ctrlname = "dmso", treatname = "plx")$data ## Not run: #GO and KEGG enrichment analysis enrich_result = EnrichAB(data, pvalue=0.05, organism="hsa") print(enrich_result$keggA$gridPlot) print(enrich_result$goA$gridPlot) ## End(Not run)