scoreInvHap: scoreInvHap: package to get inversion status of predefined...
In scoreInvHap: Get inversion status in predefined regions

Description Usage Arguments Value Examples

scoreInvHap can get the samples' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different inversion groups, R2 between the region SNPs and inversion status, heterozygote genotypes in the reference, allele frequencies in the reference population and inversion frequencies. The package include this data for 21 inversions.

This is the main function of 'scoreInvHap' package. This function accepts SNPs data in a plink or a VCF format and compute the inversion prediction. The list of available inversions is included in a GenomicRanges called 'inversionGR'.

scoreInvHap(
  SNPlist,
  inv = NULL,
  SNPsR2,
  hetRefs,
  Refs,
  R2 = 0,
  probs = FALSE,
  BPPARAM = BiocParallel::SerialParam(),
  verbose = FALSE
)

`SNPlist`	List with SNPs data from plink or `VCF-class`.
`inv`	Character with the name of the inversion to genotype. The available inversions are included in a table in the main vignette.
`SNPsR2`	Vector with the R2 of the SNPs of the region
`hetRefs`	Vector with the heterozygote form of the SNP in the inversion
`Refs`	List with the allele frequencies in the references
`R2`	Vector with the R2 between the SNPs and the inversion status
`probs`	Logical. If TRUE, scores are computed using posterior probabilities. If FALSE, scores are computed using best guess. Only applied when SNPlist is a VCF.
`BPPARAM`	A `BiocParallelParam` instance. Used to parallelize computation
`verbose`	Should message be shown?

A scoreInvHap object

# See list of inversions
data(inversionGR)
inversionGR

## Run method
if(require(VariantAnnotation)){
    vcf <- readVcf(system.file("extdata", "example.vcf", package = "scoreInvHap"), "hg19")
    res <- scoreInvHap(vcf, inv = "inv7_005")
}