pedtools (version 1.2.0)

getMap: Tabulate marker positions

Description

Return a map of the markers attached to a pedigree.

Usage

getMap(x, markers = NULL, na.action = 0, verbose = TRUE)
setMap(x, map, matchNames = NA, ...)
hasLinkedMarkers(x)

Arguments

x

An object of class ped or a list of such.

markers

A vector of names or indices referring to markers attached to x. By default, all markers are included.

na.action

Either 0 (default), 1 or 2. (See Details.)

verbose

A logical.

map

Either a data frame or the path to a map file. See Details regarding format.

matchNames

A logical; if TRUE, pre-existing marker names of x will be used to assign chromosome labels and positions from map.

...

Further arguments passed to read.table().

Value

getMap() returns a data frame with columns CHROM, MARKER and MB.

setMap() returns x with modified marker attributes.

hasLinkedMarkers() returns TRUE if two markers are located (with set position) on the same chromosome, and FALSE otherwise.

Details

The na.action argument controls how missing values are dealt with:

• na.action = 0: Return map unmodified

• na.action = 1: Replace missing values with dummy values.

• na.action = 2: Remove markers with missing data.

In setMap(), the map argument should be a data frame (or file) with the following columns in order:

1. chromosome

2. marker name

3. position (Mb)

Column names are ignored, as are any columns after the first three.

Examples

# NOT RUN {
x = singleton(1)
m1 = marker(x, chrom = 1, posMb = 10, name = "m1")
m2 = marker(x, chrom = 1, posMb = 11)
m3 = marker(x, chrom = 1)
x = setMarkers(x, list(m1, m2, m3))

# Compare effect of `na.action`
getMap(x, na.action = 0)
getMap(x, na.action = 1)
getMap(x, na.action = 2)

# Getting and setting map are inverses
y = setMap(x, getMap(x))
stopifnot(identical(x,y))

hasLinkedMarkers(x)

# }