rbind_snp_files: Combines rows of two SNP chip files and provides masking.
In stefanedwards/Siccuracy: Pipeline Package for AlphaImpute

Description Usage Arguments Details Value See Also

We distinguish between HD and LD (high and low density) SNP chips, were HD chips have priority over LD.

rbind_snp_files(hdid, ldid, hdpos, ldpos, hdfn, ldfn, fnout, outcol = NULL,
  na = 9, format = NULL, int = TRUE)

rbind_SNP_files(hdid, ldid, hdpos, ldpos, hdfn, ldfn, fnout, outcol = NULL,
  na = 9, format = NULL, int = TRUE)

`hdid`	IDs of HD genotyped individuals. Corresponds to (subset of) first column of `hdfn`.
`ldid`	IDs of LD genotyped individuals. Corresponds to (subset of) first column of `ldfn`.
`hdpos`	Integer vector of where columns in `hdfn` are positioned in output file. Coerced to same length as columns in `hdfn`.
`ldpos`	Integer vector of where columns in `ldfn` are positioned in output file. Coerced to same length as columns in `ldfn`.
`hdfn`	Filename of HD genotypes.
`ldfn`	Filename of LD genotypes.
`fnout`	Filename to write merged genotypes to.
`outcol`	Integer, number of columns in output file. When `NULL` (default), uses max value of `hdpos` and `ldpos`.
`na`	Missing values.
`format`	Character, Fortran edit descriptors for output. See parseformat.
`int`	Logical (default `TRUE`), read and write integers.

hdpos and ldpos: The output file is created with outcol columns. First, rows from hdfn are added to the file with positions described in hdpos. The first column is ignored as this is the ID column. If hdpos=c(2,3,NA,NA,4), the first two columns of hdfn are used for column 2 and 3 in the output, and the last column of hdfn is used as the 4th. The 3rd and 4th column in hdfn are ignored. This allows masking of genotypes. After hdfn is processed for rows in hdid, the same is repeated for ldfn. There is no restriction for hdfn=ldfn. The columns of the output file is prepopulated with na.