FastGO: GO analysis via clusterProfiler package

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

FastGOplot give fast way to draw GO series plot like barplot/dotplot/emapplot,Cnetplot and goplot for a enrichGO object based on clusterProfiler package.

Usage

FastGO(genes, geneList, default.universe = F, classlevel = 2:2,
  OrgDb = NULL, keyType = NULL, pAdjustMethod = "BH",
  pvalueCutoff = 0.05, qvalueCutoff = 0.05, cnet.showCategory = 5,
  verbose = TRUE, save.path = "GO", names = "love")

Arguments

genes	a character of gene id.
geneList	a numeric with id names.For example,logFoldChang with ENSEMBL id names.Note that the names of geneList must be the same type of genes
default.universe	whether to use default universe.If default.universe = F,the background genes would be provide by geneList
classlevel	Default is 2.I had tested that 2:7 was still available.If many levels is set,the process is time-consuming
OrgDb	OrgDb dataset.If NULL,use "org.Hs.eg.db"
keyType	the type of gene.Support automatically test
pAdjustMethod	the mathod of pvalue adjustment
pvalueCutoff	a list of pvalue adjust method for enrichGO
qvalueCutoff	cutoff of q value
cnet.showCategory	the number of showed cluster at cnetplot
verbose	LuckyVerbose gseplot running message or not
save.path	the sub path of saved files
names	the main path and part names of saved files

Author(s)

Weibin Huang<[e-mail]>

Examples

library(lucky)
need <- c("clusterProfiler","org.Hs.eg.db");Plus.library(need)
data(geneList, package = "DOSE")
data(geneList, package='DOSE')
universe <- unique(as.character(common.annot$ENTREZID))
system.time(
l <- FastGO(genes,
            geneList,
            classlevel = 2:2,
            OrgDb  = NULL,
            keyType = NULL,
            pAdjustMethod = "BH",
            pvalueCutoff = list(
               gseGO = 0.05,
               enrichGO = 0.05),
            qvalueCutoff  = 0.05,
            cnet.showCategory = 5,
            save.path = "GO",
            names = "love")
)
## enhanced plot
g <- enrichplot::cnetplot(goList$GOEnrichment$BP,
                          showCategory=10,
                          colorEdge=T,
                          node_label=T,
                          circular = F)
g1 <- g + theme(legend.text = element_text(face = "bold",size = 12))

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.