### Read in example ChIP-seq analyzed data output from GSE11431
### for Oct4 in ESCs directly downloaded from NCBI GEO
path <- system.file("extdata",package="GSCA")
inputfile <- read.delim(paste(path,"GSM288346_ES_Oct4.txt",sep="/"), header=FALSE,stringsAsFactors=FALSE)
### Note that 1st column is chr, 2nd and 3rd columns are starting and ending sites of peaks
### Remaining columns are other output from the peak detection algorithm
head(inputfile)
### annotatePeaks only requires the first 3 columns
annon.out <- annotatePeaks(inputfile,"mm8",10000,5000)
head(annon.out)
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