pedtools: marker_select – R documentation

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pedtools

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

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.