vcfToGenotypeMatrix: VCF file to genotype matrix
In sojwolf/ancientpca: A Probabilistic Approach to Conducting PCA with Sparse Genotype Data from Ancient Samples
Description
Usage
Arguments
Value
Description
Load vcf file into R and extract a genotype matrix (sample X SNP) coded with 0,1,2,<NA>.
Usage
1
2
vcfToGenotypeMatrix(vcf_file, max_missing_snp = 1,
max_missing_sample = 1)
Arguments
vcf_file
VCF file with genotypes only (i.e. 0/0, 0/1, etc.). Missing values can be coded as "." or "./."
max_missing_snp
Set a max. percentage of missingness per SNP allowed. Default is set to 1 (i.e. 100 percent)
max_missing_sample
Set a max. percentage of missingness per sample allowed. Default is set to 1 (i.e. 100 percent)
Value
matrix (sample x snp) coded 0,1,2, or NA
sojwolf/ancientpca documentation built on May 13, 2019, 9:53 p.m.
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Description Usage Arguments Value
Description
Load vcf file into R and extract a genotype matrix (sample X SNP) coded with 0,1,2,<NA>.
Usage
1 2 | vcfToGenotypeMatrix(vcf_file, max_missing_snp = 1,
max_missing_sample = 1)
|
Arguments
vcf_file |
VCF file with genotypes only (i.e. 0/0, 0/1, etc.). Missing values can be coded as "." or "./." |
max_missing_snp |
Set a max. percentage of missingness per SNP allowed. Default is set to 1 (i.e. 100 percent) |
max_missing_sample |
Set a max. percentage of missingness per sample allowed. Default is set to 1 (i.e. 100 percent) |
Value
matrix (sample x snp) coded 0,1,2, or NA
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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