computeDosage: computeDosage function

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

computeDosage function

Description

Convert the genotypesraw() allele patterns of 0x10001, 0x10002 (or 0x20001), 0x20002, 0 to the numbers 0, 1, 2, 9 for each marker. (Reverse, the order iff allele "1" has the minor allele frequency.)

Usage

computeDosage(markers_arg, range_arg, envir)

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
range_arg	one row of a ranges_arg. The latter is a data frame of at least three integer columns. The columns indicate a range: a chromosome number, a start base pair value, and an end base pair value.
envir	'environment' containing SQLite database and other globals especially the phenotype_table, phe.

Value

a matrix of samples X markers for all the markers that have nonzero changes.

See Also

DOfamSKATRC

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_famSKATRC(db, verbose = TRUE)
dimDosage = function(m, r, e) {print(dim(computeDosage(m, r, e)))}
applyFnToRanges(dimDosage, ENV$refRanges[50:60, ], ENV$refIndices, envir=ENV)
# This will use return dosage matrices for the markers in the ranges 50 - 60,
# but is basically ignores the results.

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