snpm2mapLD {GGtools}R Documentation

prepare input to mapLD function for haplotype block identification

Description

prepare input to mapLD function for haplotype block identification

Usage

snpm2mapLD(x, chrnum, runMAP=TRUE, ...)

Arguments

x snp.matrix instance
chrnum chromosome number
runMAP logical indicating whether or not to run mapLD
... additional arguments to mapLD

Details

sets up a data frame suitable for mapLD, and will invoke with appropriate arguments identifying columns for alleles and other identifiers if runMAP is TRUE (default).

smtest is a small snp.matrix instance

Value

a list with element struc holding the data frame, and mapLD output if requested. Note that mapLD writes an eps file to disk *sigh*.

Author(s)

Vince Carey <stvjc@channing.harvard.edu>

Examples

data(smtest)
ss = snpm2mapLD(smtest, chrnum=20, runMAP=FALSE)
ss
# you could run mapLD on ss[[1]]

[Package GGtools version 3.2.0 Index]