mixedVCFtoSnpMatrix: amalgamate called genotypes and imputed allelic dosages in...
In gQTLstats: gQTLstats: computationally efficient analysis for eQTL and allied studies
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
amalgamate called genotypes and imputed allelic dosages in VCF to
SnpMatrix representation
Usage
1
mixedVCFtoSnpMatrix(vcf, preferGT = TRUE)
Arguments
vcf
object inheriting from CollapsedVCF-class
preferGT
logical. VCF allows loci for samples to be reported in various
formats, and a given locus can have a call tagged GT and a
genotype probability or likelihood representation tagged GP or GL.
genotypeToSnpMatrix has an
uncertain parameter that, if TRUE, will transform GP or GL
content to allelic dose. Note that only the "first" dosage type appearing in the header will be transformed. Thus if GP is first in the header but
a given locus is tagged only with GL, the genotype for
thus locus will be recorded as NA.
Details
emulates output from genotypeToSnpMatrix
Value
list with elements genotypes and map
Author(s)
VJ Carey
See Also
Examples
1
2
3
4
5
fn = system.file("vcf/polytypeSNV.vcf", package="gQTLstats")
require("VariantAnnotation")
require("snpStats")
vv = readVcf(fn, genome="hg19") # only 4th SNP will have dosage coding
mixedVCFtoSnpMatrix(vv)$genotypes@.Data
gQTLstats documentation built on Nov. 8, 2020, 7:53 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
amalgamate called genotypes and imputed allelic dosages in VCF to SnpMatrix representation
Usage
1 | mixedVCFtoSnpMatrix(vcf, preferGT = TRUE)
|
Arguments
vcf |
object inheriting from |
preferGT |
logical. VCF allows loci for samples to be reported in various
formats, and a given locus can have a call tagged GT and a
genotype probability or likelihood representation tagged GP or GL.
|
Details
emulates output from genotypeToSnpMatrix
Value
list with elements genotypes and map
Author(s)
VJ Carey
See Also
Examples
1 2 3 4 5 | fn = system.file("vcf/polytypeSNV.vcf", package="gQTLstats")
require("VariantAnnotation")
require("snpStats")
vv = readVcf(fn, genome="hg19") # only 4th SNP will have dosage coding
mixedVCFtoSnpMatrix(vv)$genotypes@.Data
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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