DOpedgene: pedgene call back function

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

Description

First, ignore call backs that have less than two markers. Second, convert the genotypesraw() patterns of 0x10001, 0x10002 (or 0x20001), 0x20002, 0 from the genotype matrix to the numbers 0, 1, 2, 0 for each marker. (Reverse, the order iff allele "1" has the minor allele frequency.) Next, prepend the pedigree and person columns of the family data to this modified genotype matrix. Finally, invoke pedgene with the family data and genotype matrix for several different weights. Save the kernel and burden, value and p-value for each measurement in envir$pedgene_results.

Usage

DOpedgene(markers_arg, range_arg, 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
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

Value

None

Note

This function appends output to the data frame, envir$pedgene_results. It will print out the lines as they are generated if envir$verbose is TRUE. The data frame envir$pedgene_results is initialized by init_pedgene, and is appended to each time DOpedgene is run.

See Also

init_pedgene

Examples

db = system.file("exdata", "seqsimm.db", package="Mega2R")
ENV = init_pedgene(db)
ENV$verbose = TRUE
applyFnToRanges(DOpedgene, ENV$refRanges[50:60,], ENV$refIndices)


# donttestcheck: try this below if there is time
applyFnToGenes(DOpedgene, genes_arg = c("CEP104"))

Mega2R documentation built on Dec. 11, 2021, 9:12 a.m.