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", adjust = "BH", filename = NULL, out.dir = ".", width = 6.5, height = 4, ...)
beta |
Data frame, which contains column of 'group'. |
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). |
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 |
bp1 |
a list record enriched GO BP terms for Group1 genes in 9-Square |
bp2 |
a list record enriched GO BP terms for Group2 genes in 9-Square |
bp3 |
a list record enriched GO BP terms for Group3 genes in 9-Square |
bp4 |
a list record enriched GO BP terms for Group4 genes in 9-Square |
bp13 |
a list record enriched GO BP terms for Group1&Group3 genes in 9-Square |
bp14 |
a list record enriched GO BP terms for Group1&Group4 genes in 9-Square |
bp23 |
a list record enriched GO BP terms for Group2&Group3 genes in 9-Square |
bp24 |
a list record enriched GO BP 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
# Read beta score from gene summary table in MAGeCK MLE results