vcf2geno {trio} | R Documentation

## Transformation of VFC File

### Description

Transforms a vcf file into a matrix in genotype format required by, e.g., the functions for computing the genotypic TDT.

### Usage

    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)

### Arguments

`vcf` | a matrix resulting from reading a vcf file into `R`, or an object of class `collapsedVCF` (i.e. the output of, e.g., the function `readVcf` from the `VariantAnnotation` package). If `use.rownames = FALSE`, the column names of the genotype matrix must correspond to the personal IDs in `ped` (i.e. either the column `pid` of `ped`, if the entries in `pid` are unique, or otherwise, a combination of the columns `famid` and `pid` from `ped`, combined using an underscore). If `use.rownames = TRUE`, the column names of the genotype matrix specified by `vcf` must correspond to the row names of `ped`.
`ped` | a data frame containing the family information for the subjects in `vcf` (might also contain information for other subjects, see `allowDifference`). This data frame must contain the columns `famid`, `pid`, `fatid`, and `motid` comprising the family ID, the personal ID as well as the ID of the father and the mother, respectively.
`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 `ped` correspond to the sample names in `vcf`. For details, see `vcf`.
`allowDifference` | a logical value specifying whether `ped` and `vcf` are allowed to also contain samples not available in the respective other object. If `FALSE`, all samples in `ped` must also be available in `vcf`, and vice versa (matched as described in `vcf`). If `TRUE`, at least 10% of the samples must be contained in both `vcf` and `ped`.
`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 `none`, `one`, and `both` (which are, therefore, assumed to show more than two alleles) should be removed.
`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 `none` is coded by 0, the genotype(s) specified by `one` is coded by 1, and the genotype(s) specified by `both` is coded by 2. If for an SNV this leads to a minor allele frequency larger than 0.5 and `changeMinor = TRUE`, this 0, 1, 2-coding will be changed into a 2, 1, 0-coding.

### Value

A matrix in genotype format required, e.g., by functions for performing different types of the genotypic TDT, such as `colTDT`.

### Author(s)

Holger Schwender, holger.schwender@udo.edu

### See Also

`colTDT`, `colGxG`, `colGxE`, `ped2geno`

[Package trio version 3.28.0 Index]