setMissingGenotypes: Write a new netCDF or GDS file, setting certain SNPs to...
In GWASTools: Tools for Genome Wide Association Studies

Description Usage Arguments Details Author(s) See Also Examples

setMissingGenotypes copies an existing GDS or netCDF genotype file to a new one, setting SNPs in specified regions to missing.

1
2
3

setMissingGenotypes(parent.file, new.file, regions, file.type=c("gds", "ncdf"),
                    sample.include=NULL, compress="LZMA_RA", 
                    copy.attributes=TRUE, verbose=TRUE)

`parent.file`	Name of the parent file
`new.file`	Name of the new file
`regions`	Data.frame of chromosome regions with columns `"scanID", "chromosome", "left.base", "right.base", "whole.chrom"`.
`file.type`	The type of `parent.file` and `new.file` ("gds" or "ncdf")
`sample.include`	Vector of sampleIDs to include in `new.file`
`compress`	The compression level for variables in a GDS file (see `add.gdsn` for options).
`copy.attributes`	Logical value specifying whether to copy chromosome attributes to the new file.
`verbose`	Logical value specifying whether to show progress information.

setMissingGenotypes removes chromosome regions by setting SNPs that fall within the anomaly regions to NA (i.e., the missing value in the netCDF/GDS file). Optionally, entire samples may be excluded from the netCDF/GDS file as well: if the sample.include argument is given, only the scanIDs in this vector will be written to the new file, so the sample dimension will be length(sample.include).

For regions with whole.chrom=TRUE, the entire chromosome will be set to NA for that sample. For other regions, only the region between left.base and right.base will be set to NA.

Stephanie Gogarten

gdsSubset, anomSegStats for chromosome anomaly regions

gdsfile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
gds <- GdsGenotypeReader(gdsfile)
sample.sel <- getScanID(gds, index=1:10)
close(gds)

regions <- data.frame("scanID"=sample.sel[1:3], "chromosome"=c(21,22,23),
  "left.base"=c(14000000, 30000000, NA), "right.base"=c(28000000, 450000000, NA),
  whole.chrom=c(FALSE, FALSE, TRUE))

newgds <- tempfile()
setMissingGenotypes(gdsfile, newgds, regions, file.type="gds", sample.include=sample.sel)
file.remove(newgds)