TVTBParam-class: TVTBparam class objects
In kevinrue/TVTB: TVTB: The VCF Tool Box

Description Usage Arguments Details Value Accessor methods Author(s) See Also Examples

The TVTBparam class stores recurrent parameters of the TVTB package in a convenient format.

TVTBparam(
        genos, ranges = GRangesList(),
        aaf = "AAF", maf = "MAF", vep = "CSQ", bp = SerialParam(),
        svp = ScanVcfParam(which = reduce(unlist(ranges))))

`genos`	A `Genotypes` object that declares the three sets of homozygote reference, heterozygote, and homozygote alternate genotypes, as well as the individual key suffix used to store data for each set of genotypes in the `info` slot of a `VCF` object. See also Details section.
`ranges`	A `GRangesList` of genomic regions. See `svp` argument. In the future, may be used to facet statistics and figures.
`aaf`	INFO key suffix used to store the alternate allele frequency (AAF).
`maf`	INFO key suffix used to store the minor allele frequency (MAF).
`vep`	INFO key suffix used to extract the VEP predictions. See `svp` argument.
`bp`	A `BiocParallelParam` object.
`svp`	A `ScanVcfParam` object. If none is supplied, the `ScanVcfParam` slot `which` is automatically set to `reduce(unlist(ranges))`.

For each suffix stored in the TVTBparam object, TVTB may store data in the VCF object under the INFO keys defined as follows:

suffix: Statistics across all samples in the ExpandedVCF (e.g. "MAF").
phenotype_level_suffix: Statistics across samples associated with a given level of a given phenotype (e.g. "gender_male_MAF").

Users are recommended to avoid using those INFO keys for other purposes.

A TVTBparam object that contains recurrent parameters.

In the following code snippets x is a TVTBparam object.

genos(x), genos(x) <- value: Gets or sets the Genotypes object stored in the genos slot.
ranges(x), ranges(x) <- value: List of genomic ranges to group variants during analyses and plots.
ref(x), ref(x) <- value: Gets or sets the character vector that declares homozygote reference genotypes.
het(x), het(x) <- value: Gets or sets the character vector that declares heterozygote genotypes.
alt(x), alt(x) <- value: Gets or sets the character vector that declares homozygote alternate genotypes.
carrier(x): Gets a character vectors of concatenated heterozygote and homozygote alternate genotypes. See also het and alt accessors.
aaf(x), aaf(x) <- value: Gets or sets the INFO key suffix used to store the alternate allele frequency (AAF).
maf(x), maf(x) <- value: Gets or sets the INFO key suffix used to store the minor allele frequency (MAF).
vep(x), maf(x) <- value: Gets or sets the INFO key suffix used to extract the VEP predictions.
bp(x), bp(x) <- value: Gets or sets the BiocParallel parameters.
suffix(x): Gets a named character vector that declares individual suffixes used to store the data for each set of genotypes in the INFO field of the VCF object. Names of this vector are ref, het, alt, aaf, and maf.
svp(x), svp(x) <- value: Gets or sets the ScanVcfParam parameters.

Kevin Rue-Albrecht

Genotypes, VCF, ExpandedVCF, addCountGenos-methods vepInPhenoLevel-methods, variantsInSamples-methods, and BiocParallelParam.

# Constructors ----

grl <- GenomicRanges::GRangesList(GenomicRanges::GRanges(
    "15", IRanges::IRanges(48413170, 48434757, names = "SLC24A5")
    ))

tparam <- TVTBparam(Genotypes("0|0", c("0|1", "1|0"), "1|1"), ranges = grl)


# Accessors ----

## The Genotypes object stored in the genos slot of the TVTBparam object
## return by the genos() accessor.
genos(tparam)

## Genomic ranges stored in the TVTBparam object returned by the ranges()
## accessor.
ranges(tparam)

## Individual genotypes can be extracted with ref(), het(), alt() accessors.
ref(tparam)
het(tparam)
alt(tparam)

## Their individual INFO key suffixes can be extracted with suffix() applied to
## the above accessors.
suffix(tparam)
suffix(tparam)["ref"]
suffix(tparam)["het"]
suffix(tparam)["alt"]
suffix(tparam)["aaf"]
suffix(tparam)["maf"]

## Heterozygote, and alternate heterozygote genotypes are
## returned by the carrier() accessor.
carrier(tparam)

## INFO key suffix of alternate/minor allele frequency returned by the aaf()
## and maf() accessors.
aaf(tparam)
maf(tparam)

## INFO key suffix of the VEP predictions returned by the vep() accessor.
vep(tparam)

## BiocParallel parameters
bp(tparam)

## ScanVcfParam parameters
svp(tparam)