Description Usage Arguments Value
This function reads SNP genotype data from one or more VCF files, and returns
these as a sequence of raw SNP genotypes - effectively variant base calls -
for each sample. If all relevant input VCF files contain genotype quality
(GQ) scores for the samples of interest, these are used - along with variant
quality scores - to calculate an error probability for each SNP genotype, and
the result is returned as an array
with two slices - 'geno'
and
'prob'
- containing raw SNP genotypes and their corresponding error
probabilities, respectively. Otherwise, SNP genotypes are returned as an
array
with one slice, 'geno'
, which contains raw SNP genotype
values. In any case, the rows of each slice contain data for a given sample,
while the columns of each slice contain data for a given SNP locus.
1 2 |
... |
Input VCF file paths. |
samples |
Vector of samples for which SNP genotypes should be obtained. If not specified, genotypes are returned for all available samples. |
require.all |
Remove variants that are not completely genotyped with respect to the given samples. |
require.any |
Remove variants that do not have at least one genotype call among the given samples. |
require.polymorphic |
Remove variants that do not have at least two different genotype calls among the given samples. |
An array
object containing raw genotype data, and if available,
genotype error probabilities.
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