Nothing
create.bin <- function(file_genotype=NULL, type="text", AA=NULL, AB=NULL, BB=NULL,
availmemGb=8, dim_of_M=NULL, quiet=TRUE, missing=NULL){
## an Rcpp function to create the no-space file of the genotype data M and Mt
## from marker data. The marker data may be from an ASCII file or PLINK ped file.
## Args
## file_genotype absolute path and file name of genotype file
## AA, AB, BB numeric codes for associated genotypes in marker genotype file
## availmemGb available memory for conversion to reformatted file
## dim_of_M row, column dimensions of M.
## type where file type is text or PLINK
if(.Platform$OS.type == "unix") {
binMfile <- paste(tempdir() , "/", "M.bin", sep="")
binMtfile <- paste(tempdir() , "/", "Mt.bin", sep="")
} else {
binMfile <- paste(tempdir() , "\\", "M.bin", sep="")
binMtfile <- paste(tempdir() , "\\", "Mt.bin", sep="")
}
neededMem <- ( dim_of_M[1] * dim_of_M[1] * 8 + 2.0 *( dim_of_M[1] * dim_of_M[2] * 8 ))/( 1000000000.0) ;
if (type=="text"){
## text genotype file
if(!is.null(missing)) {
missing <- as.character(missing)
} else {
missing <- "NA"
}
# determine if M will fit in memory
# if (neededMem >= availmemGb){
# need to create M file
it_worked <- createM_BIN_rcpp(f_name = file_genotype, type=type , f_name_bin = binMfile, AA = AA, AB = AB, BB = BB,
max_memory_in_Gbytes=availmemGb, dims = dim_of_M ,
quiet = quiet, message=message , missing=missing)
if(!it_worked) # creation of ASCII file has failed
return(FALSE)
# }
message(" \n Taking transpose of marker data and writing untransposed and transposed data to disc ... \n")
createMt_BIN_rcpp(f_name_in = binMfile, f_name_out = binMtfile, type=type,
max_memory_in_Gbytes=availmemGb, dims = dim_of_M, quiet = quiet, message=message )
message("\n Writing of marker data to disc is complete ... \n")
} else {
## PLINK ped file
## using -9 to indicate missing/null genotypes
ncol <- dim_of_M[2]
# determine if M is needed
# if (neededMem >= availmemGb){
# need to create M binary file
dim_of_M[2] <- 2*dim_of_M[2] + 6 ## number of cols in a PLINK file
it_worked <- createM_BIN_rcpp(f_name = file_genotype, type=type, f_name_bin = binMfile, AA ="-9", AB = "-9", BB = "-9",
max_memory_in_Gbytes=availmemGb, dims = dim_of_M , quiet = quiet,
message=message , missing="NA")
if(!it_worked) # creation of ASCII file has failed
return(FALSE)
dim_of_M[2] <- ncol ## setting back to number of cols in no-space ASCII file
# }
message(" \n Taking transpose of marker data and writing untransposed and transposed data to disc ... \n")
createMt_BIN_rcpp(f_name_in = binMfile, f_name_out = binMtfile, type=type,
max_memory_in_Gbytes=availmemGb, dims = dim_of_M, quiet = quiet, message=message )
message(" \n Writing of marker data to disc is complete ... \n")
} ## end if else type
return(TRUE)
}
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