marker_select: Select or remove attached markers

In magnusdv/pedtools: Creating and Working with Pedigrees and Marker Data

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

Details

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

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.

See Also

setMarkers()

magnusdv/pedtools documentation built on April 9, 2024, 7:35 a.m.