align.snpdata.coding(params, snpdata, ploidy = 2, missing.snp = "fail")
ploidy
-x.$params
and $snpdata
slots, contain the
input arguments with additional columns. The input params
has
an extra
column data.coded.freq
and the input snpdata$data
has
extra column(s) for doses of the specified coded alleles.
grs.onesnp.apply
without calling
grs.make.scores
first. Note that
grs.onesnp.apply
has no way to check whether columns for
desired coded alleles are present and may return NA for codes it
cannot find.
The ploidy
argument defaults to 2, but should be set to 1 if
the input genotype data are haplotypes (either phased or male X or Y
chromosome).
The missing.snp
argument controls how to handle SNPs in the
desired paramterisation that are not present in the input genotype
data. If "okay" then SNPs listed in the desired parameterisation but
not present in the input genotype data are assumed to have dosage zero
for all individuals.
This function is one of the main computational bottlenecks and should
be aggresively optimised in future releases.
data(mthfrex)
"rs1537514_G" %in% names(mthfrex$data) # FALSE
mthfrex <- align.snpdata.coding(mthfr.params, mthfrex)$snpdata
"rs1537514_G" %in% names(mthfrex$data) # TRUE
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