EnrichSquare {MAGeCKFlute} | R Documentation |
Do enrichment analysis for selected treatment related genes in 9-squares
EnrichSquare(beta, pvalue = 0.05, enrich_method = "ORT", organism = "hsa", pathway_limit = c(3, 50), adjust = "BH", filename = NULL, out.dir = ".", width = 6.5, height = 4, ...)
beta |
Data frame, with rownames of Entrez IDs, which contains columns of 'group' and 'diff'. |
pvalue |
Pvalue cutoff. |
enrich_method |
One of "ORT"(Over-Representing Test) 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", "none". |
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. |
... |
Other available parameters in ggsave. |
A list containing enrichment results for each group genes. This list contains several elements:
kegg1 |
a list record enriched KEGG pathways for Group1 genes in 9-Square |
kegg2 |
a list record enriched KEGG pathways for Group2 genes in 9-Square |
kegg3 |
a list record enriched KEGG pathways for Group3 genes in 9-Square |
kegg4 |
a list record enriched KEGG pathways for Group4 genes in 9-Square |
kegg13 |
a list record enriched KEGG pathways for Group1&Group3 genes in 9-Square |
kegg14 |
a list record enriched KEGG pathways for Group1&Group4 genes in 9-Square |
kegg23 |
a list record enriched KEGG pathways for Group2&Group3 genes in 9-Square |
kegg24 |
a list record enriched KEGG pathways for Group2&Group4 genes in 9-Square |
go1 |
a list record enriched GO terms for Group1 genes in 9-Square |
go2 |
a list record enriched GO terms for Group2 genes in 9-Square |
go3 |
a list record enriched GO terms for Group3 genes in 9-Square |
go4 |
a list record enriched GO terms for Group4 genes in 9-Square |
go13 |
a list record enriched GO terms for Group1&Group3 genes in 9-Square |
go14 |
a list record enriched GO terms for Group1&Group4 genes in 9-Square |
go23 |
a list record enriched GO terms for Group2&Group3 genes in 9-Square |
go24 |
a list record enriched GO terms for Group2&Group4 genes in 9-Square |
Each item in the returned list has two sub items:
gridPlot |
an object created by |
enrichRes |
a enrichResult instance. |
Wubing Zhang
data(mle.gene_summary) dd = ReadBeta(mle.gene_summary, organism="hsa") p = SquareView(dd, ctrlname = "dmso", treatname = "plx") ## Not run: # Read beta score from gene summary table in MAGeCK MLE results E1 = EnrichSquare(p$data, organism="hsa") print(E1$kegg1$gridPlot) ## End(Not run)