Mega2GenABELtst: compare two gwaa.data-class objects

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

compare two gwaa.data-class objects

Description

Verify by fields, all the fields in two gwaa.data-class objects. Show more detailed marker information iff the coding values are different. (When comparing two gwaa.data-class objects, one native and one created via Mega2R sometimes when an allele frequency is .5 for both alleles, the allele order 1/2 vs 2/1 can not be currently be determined.)

Usage

Mega2GenABELtst(mega_ = mega, gwaa_ = srdta, full = TRUE, envir = ENV)

Arguments

mega_	name of first gwaa.data-class object
gwaa_	name of second gwaa.data-class object
full	if TRUE convert genotypes to text as.character(gwaa_@gtdata) and as.character(mega_@gtdata). Then standardize the order for heterozygous alleles and finally compare. This step is optional because it can be rather slow.
envir	'environment' containing SQLite database and other globals

Value

None

Examples

## Not run: 
db = system.file("exdata", "seqsimm.db", package="Mega2R")
require("GenABEL")
ENV = read.Mega2DB(db)

y = Mega2ENVGenABEL()
Mega2GenABELtst(y, y, full = FALSE)

## End(Not run)

## Not run: 
# donttestcheck: if you have more time, try ...
x = Mega2GenABEL()
Mega2GenABELtst(x, y, full = FALSE)

## End(Not run)

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