get_peaks: Output Linkage Regions

Description Usage Arguments Details Value Examples

View source: R/peaks.R

Description

Given a data.frame d with 'position' and 'value' columns output those contiguous regions where 'value' > t.

Usage

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get_peaks(d, t = 0, valcol = "lod", annot)

Arguments

d

An object of class partbl, link{npartbl}, link{famlod} or link{fampar}. Can also be a data.frame with two numeric columns that make sense as 'position' and 'value'.

t

A length-one numeric vector specifying the threshold to be used.

valcol

A length-one character vector giving the name of the column in d containing the values.

annot

A data.frame with chr, cm and bp columns.

Details

For objects of class partbl, link{npartbl}, link{famlod} or link{fampar}, the main data frame containing the LOD scores per marker is used.

Value

A data.frame where each row contains summary information about contiguous regions in d where 'value' >= t. If no regions achieve the specified t, returns NULL.

Examples

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partbl <- partbl::partbl("merlin_10_famA-parametric.tbl")
get_peaks(partbl)

bahlolab/linkrvis documentation built on June 4, 2017, 12:13 a.m.