vcf2geno {trio} | R Documentation |
Transforms a vcf file into a matrix in genotype format required by, e.g., the functions for computing the genotypic TDT.
vcf2geno(vcf, ped, none = "0/0", one = c("0/1"), both = "1/1", na.string = ".", use.rownames = FALSE, allowDifference = FALSE, removeMonomorphic = TRUE, removeNonBiallelic = TRUE, changeMinor = FALSE)
vcf |
a matrix resulting from reading a vcf file into |
ped |
a data frame containing the family information for the subjects in |
none |
a character string or vector specifying the coding for the homozygous reference genotype. |
one |
a character string or vector specifying the coding for the heterozygous genotype. |
both |
a character string or vector specifying the coding for the homozygous variant genotype. |
na.string |
a character string or vector specifying how missing values are coded in the vcf file. |
use.rownames |
a logical value specifying whether the row names of |
allowDifference |
a logical value specifying whether |
removeMonomorphic |
a logical value specifying whether monomorphic SNVs should be removed from the output. |
removeNonBiallelic |
a logical value specifying whether SNVs showing other genotypes than
the ones specified by |
changeMinor |
a logical value specifying whether the coding of the genotypes should be changed for SNVs for which the
default coding leads to a minor allele frequency larger than 0.5. The genotypes are coded by the number of minor alleles,
i.e. the genotype(s) specified by |
A matrix in genotype format required, e.g., by functions for performing different types of the genotypic TDT, such as
colTDT
.
Holger Schwender, holger.schwender@udo.edu
colTDT
, colGxG
, colGxE
, ped2geno