locusMap.list:
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.