EnrichSquare {MAGeCKFlute} | R Documentation |
Do enrichment analysis for selected treatment related genes in 9-squares
EnrichSquare( beta, id = "Gene", keytype = "Symbol", x = "Control", y = "Treatment", pvalue = 0.05, enrich_method = "ORT", organism = "hsa", limit = c(1, 120), filename = NULL, out.dir = ".", width = 6.5, height = 4, verbose = TRUE, ... )
beta |
Data frame, with columns of "Gene", "group", and "Diff". |
id |
A character, indicating the gene column in the data. |
keytype |
A character, "Symbol" or "Entrez". |
x |
A character, indicating the x-axis in the 9-square scatter plot. |
y |
A character, indicating the y-axis in the 9-square scatter plot. |
pvalue |
Pvalue cutoff. |
enrich_method |
One of "ORT"(Over-Representing Test) and "HGT"(HyperGemetric test). |
organism |
"hsa" or "mmu". |
limit |
A two-length vector (default: c(1, 120)), specifying the min and max size of pathways for enrichent analysis. |
filename |
Suffix of output file name. NULL(default) means no output. |
out.dir |
Path to save plot to (combined with filename). |
width |
As in ggsave. |
height |
As in ggsave. |
verbose |
Boolean. |
... |
Other available parameters in ggsave. |
A list containing enrichment results for each group genes. Each item in the returned list has two sub items:
gridPlot |
an object created by |
enrichRes |
a enrichResult instance. |
Wubing Zhang