IBDhaploRtools (version 1.8)

ibdhap.compare.segs: ibdhap compare segments

Description

Compares inferred ibd states with simulated "true" states. Calculates segments of ibd in the true data, giving descriptions of the segments and the proportion of correct and incorrect calls within the segments.

Usage

ibdhap.compare.segs(calls, true, data.type, seg.cutoff, pos=NA)

Arguments

calls

The data.frame created from running ibdhap.make.calls on ibd_haplo output.

true

The data frame of same dimension as calls, but with true (probably simulated) ibd states.

data.type

"h" : haplotypic data "g" : genotypic data (or hap data ran as genotypic) "r" : reduced data (output from running ibdhap.reduce.states and then ibdhap.make.states)

seg.cutoff

A scalar value between 0 and 1 to act as the cutoff value, that is, the percentage of loci in the segment whose calls must agree to call the segment for a particular ibd state.

pos

A position vector with the same length as the number of loci (rows of calls or true) describing the positions in cM, M or any other metric of each marker. If positions are not included, the segment lengths reported will be the number of markers making up a segment

Value

Returns a list containing two elememts "seg.stats", "seg.info".The "seg.stats" matrix has a row for each of the following statistics

Number of segments

Number of IBD segments

IBD segs called correctly

IBD segs called no-IBD

IBD segs called wrong IBD

IBD segs with no call

The "seg.info" matrix has a row for each segment of IBD in the true data and a column for each of the following statistics for each segment.

seg.length

true.state

seg.call

mode.call

prop.corr

Examples

## this example is taken from the package vignette,
## See vignette(IBDhaploRtools_tutorial)

data(qibd_phased)
data(ids_phased)
data(trueibd_phased)

phased.gold <- ibdhap.make.calls( qibd.file  = qibd_phased,
                   ids.file= ids_phased, cutoff = 0.8)

ibdhap.compare.segs(phased.gold, trueibd_phased, "h", 0.8, pos=NA)