run enrich_go and plot results
enrichGO_run(
deg_data,
x,
y,
cut_FC = 1,
cut_P = 0.05,
showCategory = 10,
dir = ".",
prefix = "3-EnrichGO",
OrgDb = "org.Hs.eg.db",
keyType = "SYMBOL",
ont = "ALL",
simplify = TRUE,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
qvalueCutoff = 0.2,
minGSSize = 10,
maxGSSize = 500,
readable = FALSE,
pool = FALSE,
label = c("Down", "Stable", "Up"),
label_ns = "Stable",
mc.cores = 1L
)a DEG data frame contains logFC and p value
which column is log FC
which column is P value
a single number character or numeric vector in threshold value of log FC
threshold value of P value, can set for every cut_FC number in numeric vector format
Category numbers to show
where to save results files
a prefix of file names in this step
OrgDb
keytype of input gene
One of "BP", "MF", and "CC" subontologies, or "ALL" for all three.
whether simplify
adjusted pvalue cutoff on enrichment tests to report
one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
qvalue cutoff on enrichment tests to report as significant. Tests must pass i) pvalueCutoff on unadjusted pvalues, ii) pvalueCutoff on adjusted pvalues and iii) qvalueCutoff on qvalues to be reported.
minimal size of genes annotated by Ontology term for testing.
maximal size of genes annotated for testing
whether mapping gene ID to gene Name
If ont='ALL', whether pool 3 GO sub-ontologies
symbol word for groups
which group is the stable group
param for mclapply, choose cores to use in non-Windows machine
a list result files of GO
if (FALSE) {
enrichGO_run(DEG_df, x = "log2FoldChange", y = "pvalue", dir = tempdir())
}