Nothing
validate.reference <- function(reference){
# validate reference
tmp <- (c("data.frame", "matrix", 'list') %in% class(reference))
if(!any(tmp)){
msg <- "reference should be either an external file name or a data.frame"
stop(msg)
}else{
if("matrix" %in% class(reference)){
reference <- as.data.frame(reference)
}
if('list' %in% class(reference)){
if(all(c('allele.info', 'ref.geno') %in% names(reference))){ # ref.does
if(!('data.frame' %in% class(reference$allele.info))){
msg <- 'reference$allele.info should be a data.frame'
stop(msg)
}
miss.col <- setdiff(c("Chr", "SNP", "Pos", "RefAllele", "EffectAllele"), colnames(reference$allele.info))
if(length(miss.col)==0){
# everything is fine, do nothing
}else{
msg <- paste0('Columns ', paste0(miss.col, sep=', ', collapse = ''), 'are missing in reference$allele.info', sep='')
stop(msg)
}
}else{
msg <- 'reference should contain allele.info and ref.geno if it is a list'
stop(msg)
}
}
}
if(reference.type(reference) %in% c('ref.geno', 'ref.does')){
return(NULL)
}
header <- c("bed", "bim", "fam")
tmp <- (header %in% colnames(reference))
if(!any(tmp)){
msg <- paste("Columns below were not found in reference:\n", paste(header[!tmp], collapse = " "))
stop(msg)
}
reference <- reformat.reference.path(reference)
tmp <- !file.exists(reference$bed)
if(any(tmp)){
msg <- paste(c("Files below were not found: ", reference$bed[tmp]), collapse = "\n")
stop(msg)
}
tmp <- !file.exists(reference$bim)
if(any(tmp)){
msg <- paste(c("Files below were not found: ", reference$bim[tmp]), collapse = "\n")
stop(msg)
}
tmp <- !file.exists(reference$fam)
if(any(tmp)){
msg <- paste(c("Files below were not found: ", reference$fam[tmp]), collapse = "\n")
stop(msg)
}
}
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