newMap-methods: Create a new 'Map' object.

In selectSNPs: Optimal Selection of SNPs Using a Unified Local Function

Description

This S4 function is used to create a new Map object. The input information is taken from an input DNA report in matrix format, plus a map or manifest file.

Usage

newMap(map, freq, ...)

## S4 method for signature 'data.frame,data.frame'
newMap(map, freq)

## S4 method for signature 'character,character'
newMap(map, freq, type = "C", status = 0)

Arguments

map	An input map or manifest file. A typical manifest file has the following columns: Index, Name, Chromosome, Position, GenTrain Score, SNP, ILMN Strand, Customer Strand, and NormID.
freq	An input object containing genotypes, which can be either the name of the input DNA report file name object, or a data frame containing genotypes. A DNA report file has 9 header lines (which will be skipped when reading). The column names are on the tenth lines and the genotypes start from the eleventh lines, separated by tabs.
...	Extra parameters as needed.
type	The types of a SNP, which by default is "C".
status	The status of a SNP, which by default is all 0 (i.e., non-obligatory SNPs).

Value

An Map object.

Author(s)

Nick X-L Wu

selectSNPs documentation built on Feb. 28, 2020, 5:08 p.m.