#
#Description:
# Write table with list of CpG positions on hg19, chr7
#

#To download:
#source("https://bioconductor.org/biocLite.R")
#biocLite("BSgenome.Hsapiens.UCSC.hg19") 

library(BSgenome.Hsapiens.UCSC.hg19)

#Get autosome names
chrs <- names(Hsapiens)[1:24]

#Find CpGs
cgs <- lapply(chrs, function(x) start(matchPattern("CG", Hsapiens[[x]])))
#Write data frame just for chr7
chr7_cgs <- data.frame(chrom = rep("chr7", length(cgs[[7]])), position = cgs[[7]])

#Write table
write.table(chr7_cgs, file="hg19_chr7_CGpositions.txt", sep="\t", row.names=FALSE, quote=FALSE)