genotype: Create a genotype object

In DavisBrian/seqtools: Sequence Analysis Tools

Description

This function creates a genotype object.

Usage

genotype(Z, subject.include = NULL, subject.exclude = NULL,
  snp.include = NULL, snp.exclude = NULL)

is.genotype(x)

Arguments

Z	A numeric genotype matrix (dosage matrix) or coercible with as.matrix - rows correspond to individuals and columns correspond to SNPs. Use 'NA' for missing values. The column names of this matrix should correspond to SNP names in the snpinfo object. The row names of this matrix should correspond to the id in the phenotype object.
subject.include	(optional) character vector of the subjects in rownames(Z) to be included in the analysis. See Details.
subject.exclude	(optional) character vector of the subjects in rownames(Z) to be excluded in the analysis. See Details.
snp.include	(optional) character vector of the SNPs in colnames(Z) to be included in the analysis. See Details.
snp.exclude	(optional) character vector of the SNPs in colnames(Z) to be excluded in the analysis. See Details.

Details

Z should be a numeric matrix

Typically either subject.include or subject.exclude, or both, is set to NULL. It is important to note that return include and exclude are taken from the subjects in Z and not from the input parameters.

Typically either snp.include or snp.exclude, or both, is set to NULL. It is important to note that return include and exclude are taken from the snps in Z and not from the input parameters.

Value

an object of class 'genotype'.

An object of class 'genotype' is a list containing at least the following components:

• data data frame of the data for analysis

• AAC alternate allele count.

• AAF alternate allele frequency.

• gender column name containing the gender of the subjects

• include the subjects in data that will be included is further analysis.

• exclude the subjects in data that will be excluded is further analysis.

It is important to note that return include and exclude are taken from data and not from the input parameters.

DavisBrian/seqtools documentation built on May 6, 2019, 1:56 p.m.