bdmerge {BinaryDosage}

Merge binary dosage files together

Description

Routine to merge binary dosage files together. The files don't have to be in the same format. They will be merged into a file with the format specified. Information about the SNPs, aaf, maf, avgcall, rsq, can be maintained for each file, or recalculated for the merged set.

Usage

bdmerge(
  mergefiles,
  format = 4,
  subformat = 0L,
  bdfiles,
  famfiles = character(),
  mapfiles = character(),
  onegroup = TRUE,
  bdoptions = character(),
  snpjoin = "inner"
)

Arguments

mergefiles

Vector of file names for the merged binary files. The first is the binary dosage data containing the dosages and genetic probabilities. The second file name is the family information file. The third file name is the SNP information file. The family and SNP information files are not used if the binary dosage file is in format 4. For this format the family and SNP information are in the file with the dosages and genetic probabilities.

format

The format of the output binary dosage file. Allowed values are 1, 2, 3, and 4. The default value is 4. Using the default value is recommended.

subformat

The subformat of the format of the output binary dosage file. A value of 1 or 3 indicates that only the dosage value is saved. A value of 2 or 4 indicates the dosage and genetic probabilities will be output. Values of 3 or 4 are only allowed with formats 3 and 4. If a value of zero if provided, and genetic probabilities are in the vcf file, subformat 2 will be used for formats 1 and 2, and subformat 4 will be used for formats 3 and 4. If the vcf file does not contain genetic probabilities, subformat 1 will be used for formats 1 and 2, and subformat 3 will be used for formats 3 and 4. The default value is 0.

bdfiles

Vector of binary dosage file names to be merged.

famfiles

Vector of family file names that correspond to the names in bdfiles. If the binary dosage files are all in format 4, this may be an empty character array. Default value is character().

mapfiles

Vector of map file names that correspond to the names in bdfiles. If the binary dosage files are all in format 4, this may be an empty character array. Default value is character().

onegroup

Indicator to combine all the samples in one group. If this is FALSE, the groups in each binary dosage file are maintained and any binary dosage file with one group is made into its own group. Default value is TRUE.

bdoptions

Options indicating what information to calculate and store for each SNP. These can be aaf, maf, and rsq. This option is only available if format is equal to 4 and onegroup is TRUE. Default value is character().

snpjoin

Character value that can be either "inner" or "outer". This indicates whether to do an inner or outer join of the SNPs in each binary dosage file. Default value is "inner".

Value

None

Examples

bdvcf1afile <- system.file("extdata", "vcf1a.bdose", package = "BinaryDosage")
bdvcf1bfile <- system.file("extdata", "vcf1b.bdose", package = "BinaryDosage")
mergefiles <- tempfile()

BinaryDosage:::bdmerge(mergefiles = mergefiles,
                       bdfiles = c(bdvcf1afile, bdvcf1bfile),
                       bdoptions = "maf")
bdinfo <- getbdinfo(mergefiles)