data-raw/anno.R

In ijcBIT/cnv.methyl: cnv.methyl finds copy number alteration from methylation idat files

## Upload Copy Number Polymorphism file from Broad Inst. for their exclusion

require("IlluminaHumanMethylation450kanno.ilmn12.hg19")
require("IlluminaHumanMethylationEPICanno.ilm10b2.hg19")

file <- "../20211210CUP/raw/Data/CNV_Germline_GSITIC2_BROAD_SNP6.merged.151117.hg19.CNV.txt"
cnvbroad <- read.delim(file,header=T,sep="\t")

## Add 'chr' tag in front of chr numbers
cnvbroad <- data.frame(chr=paste("chr",cnvbroad$Chromosome,sep = ""), start=cnvbroad$Start, end=cnvbroad$End)

## make Granges object:
cnvbroadgr <- regioneR::toGRanges(cnvbroad)
Exclude <- cnvbroadgr

#Remove chr23 (X) and chr24 (Y)
Exclude <- GenomeInfoDb::keepSeqlevels(Exclude, paste("chr",c(1:22), sep=""), pruning.mode="coarse")
seqnames(Exclude)

## Bed file CancerGenes most amplified/most deleted in cancer autosomal chromosomes
data("CancerGenes")
detail_region <- regioneR::toGRanges(CancerGenes)
seqlevels(detail_region)

#450k annotation:
anno_450K <- conumee::CNV.create_anno(array_type = "450k",chrXY = F,
                        exclude_regions = Exclude, detail_regions = detail_region)
anno_450K@probes$Name <-IlluminaHumanMethylation450kanno.ilmn12.hg19::Other[names(anno_450K@probes),"UCSC_RefGene_Name"]
#Epic annotation:
anno_epic <- conumee::CNV.create_anno(array_type = "EPIC",chrXY = F,
                                      exclude_regions = Exclude, detail_regions = detail_region)
anno_epic@probes$Name <-IlluminaHumanMethylationEPICanno.ilm10b2.hg19::Other[names(anno_epic@probes),"UCSC_RefGene_Name"]
#Overlap annotation:
anno_overlap <- conumee::CNV.create_anno(array_type = "overlap",chrXY = F,
                                      exclude_regions = Exclude, detail_regions = detail_region)
cgs <- names(anno_overlap@probes)

anno_overlap@probes$Name<-sapply(
  unname(sapply(
    paste0(anno_epic@probes[cgs,]$Name,";" ,anno_450K@probes[cgs,]$Name),
    function(g) unique(strsplit(g, split = ";")[[1]])
    )),function(x) paste(x,collapse = ";")
  )
rm("file","cnvbroad","cnvbroadgr","Exclude","CancerGenes")
# mcols(anno_overlap@probes) <- [names(anno_overlap@probes),"UCSC_RefGene_Name"]
# #saveRDS(anno, "./data-raw/anno.rds")
# #usethis::use_data(anno, overwrite = TRUE,internal = TRUE)