getQTLPeaks: Get QTL peaks.

In gact/shmootl: QTL Analysis Utilities for Yeast

Description

Get QTL peaks.

Usage

## Generic method.
getQTLPeaks(x, chr=NULL, ...)

## S3 method for class 'mapframe'
getQTLPeaks(x, chr = NULL, threshold = NULL,
  lodcolumn = NULL, ...)

## S3 method for class 'qtl'
getQTLPeaks(x, chr = NULL, qtl.indices = NULL, ...)

## S3 method for class 'scanone'
getQTLPeaks(x, chr = NULL, threshold = NULL,
  lodcolumn = NULL, ...)

Arguments

x	An R/qtl scanone or qtl object.
chr	Vector indicating which sequences to consider. If no sequences are specified, QTL peaks are returned for all available sequences.
...	Further arguments (see below).
threshold	For a scanone or equivalent object, this contains a single numeric LOD significance threshold, or an object (e.g. summary.scanoneperm) containing one such threshold and its associated significance level.
lodcolumn	In a scanone or equivalent object, this parameter indicates which LOD column to consider. In other objects with LOD-column-associated elements, this parameter indicates which LOD-column-associated element to consider. This must be either a LOD column name or an index with respect to the set of LOD columns. If no LOD column is specified and one such column is found, that column is used by default; otherwise a LOD column must be specified.
qtl.indices	In a qtl object, this option indicates the QTLs for which a QTL peak should be returned.

Value

A mapframe object in which each row indicates the locus of a QTL peak, with row names containing respective QTL names. Returns an empty mapframe if there are no significant QTLs.

See Also

Other QTL functions: estPhysicalPositions, getQTLFeatures, getQTLIntervals, plotQTLScanone

gact/shmootl documentation built on Nov. 11, 2021, 6:23 p.m.