scoreInvHapRes-class: scoreInvHapRes instances

Description Usage Arguments Value Methods (by generic) Slots Examples

Description

Container with the results of the classification pipeline

Usage

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## S4 method for signature 'scoreInvHapRes'
classification(object, minDiff = 0, callRate = 0, inversion = TRUE)

## S4 method for signature 'scoreInvHapRes'
certainty(object)

## S4 method for signature 'scoreInvHapRes'
diffscores(object)

## S4 method for signature 'scoreInvHapRes'
maxscores(object)

## S4 method for signature 'scoreInvHapRes'
numSNPs(object)

## S4 method for signature 'scoreInvHapRes'
plotCallRate(object, callRate = 0.9, ...)

## S4 method for signature 'scoreInvHapRes'
plotScores(object, minDiff = 0.1, ...)

## S4 method for signature 'scoreInvHapRes'
propSNPs(object)

## S4 method for signature 'scoreInvHapRes'
scores(object)

Arguments

object

scoreInvHapRes

minDiff

Numeric with the threshold of the minimum difference between the top and the second score. Used to filter samples.

callRate

Numeric with the threshold of the minimum call rate of the samples. Used to filter samples.

inversion

Logical. If true, haplotypes classification is adapted to return inversion status. (Default: TRUE)

...

Further parameters passed to plot function.

Value

A scoreInvHapRes instance

Methods (by generic)

Slots

classification

Factor with the individuals classification

scores

Simmilarity scores for the different haplotypes.

numSNPs

Numeric with SNPs used to compute the scores.

certainty

Numeric with the certainty of the classification for each individual.

Examples

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if(require(VariantAnnotation)){
    vcf <- readVcf(system.file("extdata", "example.vcf", package = "scoreInvHap"), "hg19")

    ## Create scoreInvHapRes class from pipeline
    res <- scoreInvHap(vcf, inv = "inv7_005")

    ## Print object
    res

    ## Get haplotype classification
    classification(res)

    ## Get similiraty scores
    scores(res)
}

scoreInvHap documentation built on Feb. 6, 2021, 2 a.m.