locusMap.list {CGEN} | R Documentation

## List to describe the locus map data

### Description

The list to describe the locus map data for `Manhattan.plot`.

### Format

The format is: List of 8

file

  File containing the locus map data. This file must contain at least three columns: a column for the SNP names, a column for the chromosomes, and a column for the location of the SNP on the chromosome. The location should be numeric values. No default.

file.type

  1, 3 or 4 (see details). The default is 3.

delimiter

  The delimiter used in the files. The default is "\t" (a tab).

header

  0 or 1 if the file contains a header of variable names. The default is 0.

snp.var

  Variable name (e.g. rs number) or column number of the SNP (locus) variable. No default.

chrm.var

  Variable name (e.g. chromosome number) or column number of the chromosome variable. No default.

loc.var

  Variable name or column number of the location variable, which denotes the SNP's position on the chromosome. This variable should be numeric. No default.

### Details

In this list, `file` must be specified. The types of files are described below.

- `Type 1` An .rda file where the saved object was a data frame.

- `Type 3` A delimited file.

[Package CGEN version 3.18.0 Index]