vcf_to_matrix: VCF To Matrix
In AndersenLab/cegwas: A set of functions to process phenotype data, perform GWAS, and perform post-mapping data processing for C. elegans.
Description
Usage
Arguments
Value
See Also
Description
vcf_to_matrix converts variant calls from a bcf, vcf.gz or vcf file into an R dataframe.
Uses only biallelic variants. Heterozygous calls are ignored. Requires bcftools.
Usage
1
vcf_to_matrix(vcf, allele_freq = 0, tag_snps = NA, region = NA)
Arguments
vcf
a bcf, vcf, or vcf.gz file
allele_freq
allele frequency to filter on. Default is 0
region
A region to subset on.
tag_snips
A set of variants to filter on. By default, all variants are taken.
Value
Matrix of genotype calls
See Also
generate_kinship generate_mapping
AndersenLab/cegwas documentation built on March 6, 2020, 1:10 a.m.
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Description Usage Arguments Value See Also
Description
vcf_to_matrix converts variant calls from a bcf, vcf.gz or vcf file into an R dataframe.
Uses only biallelic variants. Heterozygous calls are ignored. Requires bcftools.
Usage
1 | vcf_to_matrix(vcf, allele_freq = 0, tag_snps = NA, region = NA)
|
Arguments
vcf |
a bcf, vcf, or vcf.gz file |
allele_freq |
allele frequency to filter on. Default is 0 |
region |
A region to subset on. |
tag_snips |
A set of variants to filter on. By default, all variants are taken. |
Value
Matrix of genotype calls
See Also
generate_kinship generate_mapping
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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