Mega2GenABELtst: compare two gwaa.data-class objects

Description Usage Arguments Value Examples

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

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
## 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 Oct. 23, 2020, 8:19 p.m.