pedtools (version 1.1.0)

marker_select: Select or remove attached markers

Description

Functions for manipulating markers attached to ped objects.

Usage

selectMarkers(x, markers = NULL, chroms = NULL, fromPos = NULL, toPos = NULL)
getMarkers(x, markers = NULL, chroms = NULL, fromPos = NULL, toPos = NULL)
removeMarkers(x, markers = NULL, chroms = NULL, fromPos = NULL, toPos = NULL)
whichMarkers(x, markers = NULL, chroms = NULL, fromPos = NULL, toPos = NULL)

Arguments

x

A ped object, or a list of such

markers

Either a character vector (with marker names), a numeric vector (with marker indices), a logical (of length nMarkers(x)), or NULL.

chroms

A vector of chromosome names, or NULL

fromPos

A single number or NULL

toPos

A single number or NULL

Value

The return values of these functions are:

• selectMarkers(): an object identical to x, but where only the indicated markers are kept

• removeMarkers(): an object identical to x, but where the indicated markers are removed

• getMarkers(): a list of marker objects. Note: If x is a list of pedigrees, the marker objects attached to the first component will be returned.

• whichMarkers(): an integer vector with indices of the indicated markers. If x is a list of pedigrees an error is raised unless whichMarkers() gives the same result for all components.

Details

If markers consists of negative integers, it will be converted to its complement within 1:nMarkers(x).

See Also

setMarkers()