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", 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), "DAVID", "GOstats", and "HGT"(HyperGemetric test). |
organism |
A character, specifying organism, such as "hsa" or "Human"(default), and "mmu" or "Mouse" |
adjust |
One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". |
filename |
Suffix of output file name. NULL(default) means no output. |
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
, bpA
, bpB
. 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_Data) # Read beta score from gene summary table in MAGeCK MLE results