scoreInvHapRes-class: scoreInvHapRes instances

In isglobal-brge/snpfier: Get inversion status in predefined regions

Description

Container with the results of the classification pipeline

Usage

## 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)

• classification: Get classification

• certainty: Get classification certainty

• diffscores: Get maximum similarity scores

• maxscores: Get maximum similarity scores

• numSNPs: Get number of SNPs used in computation

• plotCallRate: Plot call rate based QC

• plotScores: Plot scores based QC

• propSNPs: Get proportions of SNPs used in computation

• scores: Get similarity scores

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

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)
}

isglobal-brge/snpfier documentation built on Feb. 10, 2021, 3:29 a.m.