GO Enrichment on Two Differential Expression Integration Results.

DEbDEFE(
  de.de,
  de.fe.key,
  out.folder = NULL,
  gene.type = c("ENSEMBL", "ENTREZID", "SYMBOL"),
  go.type = c("ALL", "BP", "MF", "CC"),
  enrich.pvalue = 0.05,
  enrich.qvalue = 0.05,
  species = c("Human", "Mouse", "Rat", "Fly", "Arabidopsis", "Yeast", "Zebrafish",
    "Worm", "Bovine", "Pig", "Chicken", "Rhesus", "Canine", "Xenopus", "Anopheles",
    "Chimp", "E coli strain Sakai", "Myxococcus xanthus DK 1622"),
  padj.method = c("BH", "holm", "hochberg", "hommel", "bonferroni", "BY", "fdr",
    "none"),
  show.term = 15,
  str.width = 30,
  plot.resolution = 300,
  plot.width = 7,
  plot.height = 9,
  save = TRUE
)

Arguments

de.de	Dataframe contains integrated results of two differential expression analysis of RNA-seq.
de.fe.key	The key type of integrated results ("Type" column of `de.de`) to perform functional enrichment.
out.folder	Folder to save enrichment results. Default: wording directory.
gene.type	Gene name type of `DE1_Gene` column. Chosen from ENSEMBL, ENTREZID,SYMBOL. Default: ENSEMBL.
go.type	GO enrichment type, chosen from ALL, BP, MF, CC. Default: ALL.
enrich.pvalue	Cutoff value of pvalue. Default: 0.05.
enrich.qvalue	Cutoff value of qvalue. Default: 0.05.
species	Species used, chosen from "Human","Mouse","Rat","Fly","Arabidopsis","Yeast","Zebrafish","Worm","Bovine","Pig","Chicken","Rhesus", "Canine","Xenopus","Anopheles","Chimp","E coli strain Sakai","Myxococcus xanthus DK 1622". Default: "Human".
padj.method	One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". Default: BH.
show.term	Number of enrichment term to show. Default: 15.
str.width	Length of enrichment term in plot. Default: 30.
plot.resolution	Resolution of plot. Default: 300.
plot.width	The width of plot. Default: 7.
plot.height	The height of plot. Default: 9.
save	Logical value, whether to save all results. Default: TRUE.

Value

If save is TRUE, return NULL (all results are in out.folder), else retutn result dataframe.

Examples

library(DEbPeak)
rna.diff.file <- system.file("extdata", "RA_RNA_diff.txt", package = "DEbPeak")
de1.res <- read.table(file = rna.diff.file, header = TRUE, sep = "\t")
de2.res <- read.table(file = rna.diff.file, header = TRUE, sep = "\t")
# use same file as example
de.de <- DEbDE(de1.res = de1.res, de2.res = de2.res, de1.l2fc.threshold = 0.5, de2.l2fc.threshold = 1)
#> Differential expression analysis with DESeq2!
#> Differential expression analysis with DESeq2!
de.de.fe <- DEbDEFE(de.de = de.de, de.fe.key = "Down_Down", gene.type = "SYMBOL", go.type = "BP", species = "Mouse", save = F)
#> Convert SYMBOL to ENTREZID!
#> 'select()' returned 1:1 mapping between keys and columns
#> Warning: 5.76% of input gene IDs are fail to map...
#> conduct BP GO enrichment analysis.
#> wrong orderBy parameter; set to default `orderBy = "x"`
#> Scale for y is already present.
#> Adding another scale for y, which will replace the existing scale.