scoreInvHapRes {scoreInvHap} | R Documentation |
Container with the results of the classification pipeline
## S4 method for signature 'scoreInvHapRes' classification(object, minDiff = 0, callRate = 0, inversion = FALSE) ## 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)
object |
|
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. |
... |
Further parameters passed to plot function. |
A scoreInvHapRes instance
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
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.
if(require(VariantAnnotation)){ vcf <- readVcf(system.file("extdata", "example.vcf", package = "scoreInvHap"), "hg19") ## Create scoreInvHapRes class from pipeline res <- scoreInvHap(vcf, SNPsR2$inv7p11.2, hetRefs = hetRefs$inv7p11.2, Refs$inv7p11.2) ## Print object res ## Get haplotype classification classification(res) ## Get similiraty scores scores(res) }