ChIPseeker.R

library(clusterProfiler)
library(enrichplot)
library(ggplot2)
library(org.Hs.eg.db)

setwd("TCGA-BRCA/")
xxt<-read.table("selectmrna43_fc")
head(xxt)
genelist<-as.numeric(xxt[,3])
names(genelist) = as.character(rownames(xxt))
genelist = sort(genelist, decreasing = TRUE)
gse <- gseGO(geneList=genelist, 
             ont ="BP", 
             keyType = "ENSEMBL", 
             minGSSize = 3, 
             pvalueCutoff = 0.05, 
             verbose = TRUE, 
             OrgDb = org.Hs.eg.db, 
             pAdjustMethod = "none")

y<-as.data.frame(x)
p<-ggplot(y[c(3,5,6,9,18,20,26,33),],
             aes(x = GeneRatio, y = Description)) + 
             geom_point(aes(size = GeneRatio, color = p.adjust)) +
             theme_bw(base_size = 14) +
             scale_colour_gradient(limits=c(0, 0.10), low="red") +
             ylab(NULL)

library(ChIPseeker)
library(GSEABase)
file <- "biomartpeaks"
gr <- readPeakFile(file)

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
TxDb <- TxDb.Hsapiens.UCSC.hg19.knownGene
genes <- seq2gene(gr,
                  tssRegion = c(-1000,1000),
                  flankDistance = 3000,
                  TxDb)   //nice TxDb, file<-sys.arg[]
  403 genes were dropped because they have exons located on both strands of the same
  reference sequence or on more than one reference sequence, so cannot be
  represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object,
  or use suppressMessages() to suppress this message.   //so it's fine to drop genes

g <- bitr(genes,
          "ENTREZID",
          "SYMBOL",