vcf2snpmatrix: convert a vcf file to snpMatrix object 'vcf2snpmatrix'...
In ollyburren/cupcake: PCA for GWAS
Description
Usage
Arguments
Value
Description
convert a vcf file to snpMatrix object
vcf2snpmatrix convert a vcf file to snpMatrix object
Usage
1
vcf2snpmatrix(vcf, bcft, region_file, quiet = TRUE)
Arguments
vcf
a scalar - path to vcf file
bcft
a scalar - path to bcftools binary
region_file
a scalar - path to a file satisfying -R bcftools criteria (optional)
quiet
a boolean - if set to false then debug information shown (default = FALSE)
Value
a list with two slots. sm is the snpMatrix object and info is a data.table describes SNPs
ollyburren/cupcake documentation built on July 30, 2020, 9:58 a.m.
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Description Usage Arguments Value
Description
convert a vcf file to snpMatrix object
vcf2snpmatrix convert a vcf file to snpMatrix object
Usage
1 | vcf2snpmatrix(vcf, bcft, region_file, quiet = TRUE)
|
Arguments
vcf |
a scalar - path to vcf file |
bcft |
a scalar - path to bcftools binary |
region_file |
a scalar - path to a file satisfying -R bcftools criteria (optional) |
quiet |
a boolean - if set to false then debug information shown (default = FALSE) |
Value
a list with two slots. sm is the snpMatrix object and info is a data.table describes SNPs
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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