R/Merge.R

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

# not used yet

merge_Vcf <- function(...){
    vcfs <- list(...)
    for(i in vcfs){
        if(!inherits(i, "vcfR")) stop("Only VCFs supported")
    }

    if(length(vcfs) == 1){
        return(vcfs[[1]])
    } else if(length(vcfs) >= 2){
        vcf <- vcfs[[1]]
        for(i in 2 : length(vcfs)){
            vcfi <- vcfs[[i]]
            if(ncol(vcf@gt) == ncol(vcfi@gt)){
                if(all(colnames(vcf@gt) %in% colnames(vcfi@gt)) &
                   all(colnames(vcfi@gt) %in% colnames(vcf@gt))){
                    vcf@fix <- rbind(vcf@fix, vcfi@fix)
                    vcf@gt <- rbind(vcf@gt, vcfi@gt)
                } else {
                    stop("Samples in all files should be same")
                }
            } else {
                stop("Samples in all files should be same")
            }
        }
    }

    return(vcf)
}

# # not used yet
# merge_plink <- function(...){
#     files <- list(...)
#     for(i in files){
#         if(!inherits(i, "list")){stop("Were all inputs p.link ?")}
#     }
#     if(length(files) == 1){
#         return(files[[1]])
#     } else if(length(files) >= 2){
#         f <- files[[1]]
#         # for(i in 2 : length(files)){
#         #     fi <- files[[i]]
#         #     if(ncol(vcf@gt) == ncol(vcfi@gt)){
#         #         if(all(colnames(vcf@gt) %in% colnames(vcfi@gt)) &
#         #            all(colnames(vcfi@gt) %in% colnames(vcf@gt))){
#         #             vcf@fix <- rbind(vcf@fix, vcfi@fix)
#         #             vcf@gt <- rbind(vcf@gt, vcfi@gt)
#         #         } else {
#         #             stop("Samples in all files should be same")
#         #         }
#         #     } else {
#         #         stop("Samples in all files should be same")
#         #     }
#         # }
#     }
#
#     return(vcf)
# }