Quite often subjects have their genotypes imputed in batches. The
files returned by these imputation can be converted into binary dosage
files. These binary files can be merged into a single file if they have
the same SNPs and different subjects using the bdmerge routine.
bdmerge
The bdmerge routine takes the following parameters
- mergefiles - A character vector of the binary dosage file, family
file, and map file names
- format - Integer value indicating which format of the binary dosage
file should be used for the merged files
- subformat - Integer value indicating which subformat should be used
for the merged files
- bdfiles - A character vector of the binary dosage files to
merge
- famfiles - Character vector of the family files associated with the
binary dosage files to merge
- mapfiles - Character vector of the map files associated with the
binary dosage files to merge
- onegroup - Logical value indicating if the binary dosage saves SNP
summary information about each merged file
- bdoptions - Character vector indicating on which SNP information
should be evaluated for the merged files. This cannot be used if
onegroup is set to FALSE
- snpjoin - Character value indicating if an inner or outer join is
done for the SNPs
The following code merges vcf1a.bdose and
vcf1b.bdose into one binary dosage file. It then displays the
number of subjects in each file.
bd1afile <- system.file("extdata", "vcf1a.bdose", package = "BinaryDosage")
bd1bfile <- system.file("extdata", "vcf1b.bdose", package = "BinaryDosage")
bd1file <- tempfile()
bdmerge(mergefiles = bd1file, bdfiles = c(bd1afile, bd1bfile))
bd1ainfo <- getbdinfo(bd1afile)
bd1binfo <- getbdinfo(bd1bfile)
bd1info <- getbdinfo(bd1file)
nrow(bd1ainfo$samples)
#> [1] 60
nrow(bd1binfo$samples)
#> [1] 40
nrow(bd1info$samples)
#> [1] 100