ReadMap {Eagle}

Read map file

Description

Read in the marker map data.

Usage

ReadMap(filename = NULL, header = TRUE, ...)

Arguments

filename

contains the name of the map file. The file name needs to be in quotes. If the file is not in the working directory, then the full path to the file is required.

header

a logical value. When TRUE, the first row of the file contains the column headings.

...

arguments to be passed to read.table such as skip, sep. See read.table so the list of arguments.

Details

Association mapping, unlike classical linkage mapping, does not require a map to find marker-trait associations. So, reading in a map file is optional. If a map file is supplied, then the marker names from this file are used when reporting the findings from AM. If a map file is not supplied, then generic names M1, M2, ..., are assigned to the marker loci where the number refers to the column number in the marker file.

A space separated text file with column headings is assumed as the default input. The map file can have three or four columns. If the map file has three columns, then it is assumed that the three columns are the marker locus names, the chromosome number, and the map position (in any units). If the map file has four columns as with a 'PLINK map file, then the columns are assumed to be the marker locus names, the chromosome number, the map position in centimorgans, and the map position in base pairs.

Missing values are allowed but not in the first column of the file (i.e. the marker labels are not allowed to be missing).

The order of the marker loci in this file is assumed to be the same order as the loci in the marker data file.

The first column of the map file is assumed to contain the marker names.

Value

a data frame is returned of the map data.

See Also

ReadMarker and ReadPheno.

Examples

# Read in  example map data from ./extdata/

# find the full location of the map data 
complete.name <- system.file('extdata', 'map.txt', package='Eagle')
  
# read in map data 
map_obj <- ReadMap(filename=complete.name) 
                               
# look at first few rows of the map file
head(map_obj)