IBDhaploRtools (version 1.8)

ibdhap.make.calls: ibdhap.make.calls

Description

Stores and simplifies the qibd files created by IBD Haplo by "calling" a marker to be in an ibd state if it's marginal probability meets some "cutoff" value, a zero or "no call" is assigned to a marker in which no single state meets the value assigned to "cutoff". The R data.frame that this function creates is expected by other functions in this package.

Usage

ibdhap.make.calls(qibd.filename = NULL, ids.filename = NULL, qibd.file
= NULL, ids.file = NULL, cutoff = 0.8)

Arguments

qibd.file

A matrix of the contents of the qibd.out file the is produced from running ibd_haplo. If this is left as the default NULL, qibd.filename should be specified

qibd.filename

The filename (location) of the qibd.out file the is produced from running ibd_haplo. This is to be input as a character string. The qibd file will be loaded from this location if qibd.file is not specified.

ids.file

A matrix of the .ids file used to run ibd_haplo.If this is left as the default NULL, ids.filename should be specified

ids.filename

The filename (location) of the ids file used to run ibd_haplo. This is to be input as a character string. The ids file will be loaded from this location if ids.file is not specified.

cutoff

A scalar value between 0 and 1 to act as the "cutoff" value. This is the value which, if the maximum marginal probability of an ibd state is greater than, that marker will be called that state. Otherwise, the marker is called as zero, which in this context, means that there was not evidence enough to determine the specific ibd state of that marker. Default value is 0.8.

Value

Returns a data.frame with ncol = # of sets of haplotypes/ pairs of genotypes in the qibd file. nrow = # of markers/SNPs Each column of this data.frame consists of integers (0 - 15 for haplotypes, 0-9 for genotypic data) corresponding to the ibd state at that marker (if the probability of that state for the marker is maximal and exceeds "cutoff" value, or a 0 value (for no call).

Examples

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

data(qibd_phased)
data(ids_phased)

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

## alternatively, specify the file location, e.g.
## qibd.filename <- '~/Documents/qibd_unphased_2011.gold'
## ids.filename <- '~/Documents/ids_unphased_2011.gold'
## phased.gold <- ibdhap.make.calls( qibd.filename = qibd.filename, 
##                   ids.filename = ids.filename, cutoff = 0.8)