getgenotypes_R: fetch genotype matrix for specified markers (assemble by...

In Mega2R: Accessing and Processing a 'Mega2' Genetic Database

fetch genotype matrix for specified markers (assemble by rows)

Description

This function calls the C++ function that does all the heavy lifting. It passes the locus_index and the locus_offset in the unified_genotype_table from the markers_arg argument. It also gathers other data.frames that are in the "global" ENV environment. One frame contains a bit vector of compressed genotype information, another contains the alleles for each marker, and finally there are some bookkeeping related data. Note this function is for Testing only and is not exported.

Usage

getgenotypes_R(markers_arg, sepstr = "", envir = ENV)

Arguments

markers_arg	a data.frame with the following 5 observations: locus_link is the ordinal ranking of this marker among all loci locus_link_fill is the position of corresponding genotype data in the unified_genotype_table MarkerName is the text name of the marker chromosome is the integer chromosome number position is the integer base pair position of marker
sepstr	separator string for alleles (default is none)
envir	an environment that contains all the data frames created from the SQLite database.

Details

The unified_genotype_table contains one raw vector for each person. In the vector there are two bits for each genotype. This function creates an output matrix by selecting from each row all the needed markers and then repeating for each person.

Value

a matrix of genotypes represented as a nucleotide pair. There is one column for each marker in markers_arg argument. There is one row for each person in the family (fam) table.

Examples

## Not run: 
# genotypes for all persons in markers data.frame argument
getgenotypes_R(ENV$markers)

# genotypes for all persons in chromosome n
getgenotypes_R(ENV$markers[ENV$markers$chromosome == n,])

## End(Not run)

Mega2R documentation built on May 29, 2024, 1:14 a.m.