filter_geno: Filters genotypes based on various criteria
In funkhou9/snpTools: Miscellaneous tools for working with SNP genotyping data
Description
Usage
Arguments
Value
Description
Before using genotypes in models, this function can be used to filter out SNPs that are
fixed, have a low call rate, etc.
Usage
1
filter_geno(geno, call_rate = 0.9, fix = TRUE)
Arguments
geno
matrix of genotyping data with individuals in rows and SNPs in columns.
Formatted in dosage of B format.
call_rate
numeric proportion indicating the call rate that must be met
fix
boolean. If TRUE, remove SNPs that are fixed among all animals
Value
geno matrix with removed (filtered out) SNPs
funkhou9/snpTools documentation built on May 16, 2019, 4:05 p.m.
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Description Usage Arguments Value
Description
Before using genotypes in models, this function can be used to filter out SNPs that are fixed, have a low call rate, etc.
Usage
1 | filter_geno(geno, call_rate = 0.9, fix = TRUE)
|
Arguments
geno |
matrix of genotyping data with individuals in rows and SNPs in columns. Formatted in dosage of B format. |
call_rate |
numeric proportion indicating the call rate that must be met |
fix |
boolean. If TRUE, remove SNPs that are fixed among all animals |
Value
geno matrix with removed (filtered out) 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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