mpMap2 (version 1.0.4)

as.mpInterval: Convert mpcross object to MPWGAIM format

Description

Convert an object of class mpcrossMapped to the format used by MPWGAIM.

Usage

as.mpInterval(
  object,
  type = "mpMarker",
  positions,
  homozygoteMissingProb,
  heterozygoteMissingProb,
  errorProb
)

Arguments

object

The object of class mpcrossMapped to convert

type

The type of MPWGAIM object to output. Must be "mpMarker" or "mpInterval"

positions

In the case of mpMarker format, the positions at which the IBD probabilities should be output. Must be either "all" (all positions for which IBD probabilities are available) or "marker" (only marker positions).

homozygoteMissingProb

Used as an input to computeGenotypeProbabilitiesInternal, if the IBD probabilities need to be calculated.

heterozygoteMissingProb

Used as an input to computeGenotypeProbabilitiesInternal, if the IBD probabilities need to be calculated.

errorProb

Used as an input to computeGenotypeProbabilitiesInternal, if the IBD probabilities need to be calculated.

Value

An object of class mpMarker or mpInterval, which are formats specified by package mpwgaim.

Details

MPWGAIM is a package for performing QTL analysis using multi-parent populations. This function outputs a data object suitable for input to MPWGAIM. The output object can be in MPWGAIMs mpMarker or mpInterval formats. See the documentation of MPWGAIM for further information.