R/AllGenerics.R

In kevinrue/TVTB: TVTB: The VCF Tool Box

# pairInfo ----

setGeneric(
    "pairsInfo", signature = c("vcf"),
    function(vcf, metric, phenotype, ..., title = metric)
        standardGeneric("pairsInfo")
)

# plotInfo ----

setGeneric(
    "plotInfo", signature = c("vcf"),
    function(
        vcf, metric, range, annotation, phenotype,
        type = c("p", "heatmap"), zero.rm = FALSE)
        standardGeneric("plotInfo")
)

# autodetectGenotypes ----

setGeneric(
    "autodetectGenotypes", signature = c("vcf"),
    function(vcf)
        standardGeneric("autodetectGenotypes")
)

# dropInfo ----

setGeneric(
    "dropInfo", signature = "vcf",
    function(vcf, key = NULL, slot = "both")
        standardGeneric("dropInfo")
)

# addOverallFrequencies ----

setGeneric(
    "addOverallFrequencies", signature = c("vcf"),
    function(vcf, force = FALSE)
        standardGeneric("addOverallFrequencies")
)

# addPhenoLevelFrequencies ----

setGeneric(
    "addPhenoLevelFrequencies", signature = c("vcf"),
    function(vcf, pheno, level, force = FALSE)
        standardGeneric("addPhenoLevelFrequencies")
)

# addPhenotypeFrequencies ----

setGeneric(
    "addFrequencies", signature = c("vcf", "phenos"),
    function(vcf, phenos, force = FALSE)
        standardGeneric("addFrequencies")
)

# addCountGenos ----

setGeneric(
    "addCountGenos", signature = "vcf",
    function(
        vcf, genos, key, description, samples = 1:ncol(vcf), force = FALSE)
        standardGeneric("addCountGenos")
)

# countGenos ----

setGeneric(
    "countGenos", signature = "x",
    function(x, genos, pheno = NULL, level = NULL)
        standardGeneric("countGenos")
)

# variantsInSamples ----

setGeneric(
    "variantsInSamples", signature = c("vcf"),
    function(vcf, samples = 1:ncol(vcf), unique = FALSE)
        standardGeneric("variantsInSamples")
)

# vepInPhenoLevel ----

setGeneric(
    "vepInPhenoLevel", signature = c("vcf"),
    function(vcf, phenoCol, level, vepCol, unique = FALSE)
        standardGeneric("vepInPhenoLevel")
)

# TVTBparam class ----

setGeneric(
    "genos", signature = "x",
    function(x)
        standardGeneric("genos")
)

setGeneric(
    "genos<-", signature = c("x", "value"),
    function(x, value)
        standardGeneric("genos<-")
)

setGeneric(
    "aaf", signature = "x",
    function(x)
        standardGeneric("aaf")
)

setGeneric(
    "aaf<-", signature = c("x", "value"),
    function(x, value)
        standardGeneric("aaf<-")
)

setGeneric(
    "maf", signature = "x",
    function(x)
        standardGeneric("maf")
)

setGeneric(
    "maf<-", signature = c("x", "value"),
    function(x, value)
        standardGeneric("maf<-")
)

setGeneric(
    "het", signature = "x",
    function(x)
        standardGeneric("het")
)

setGeneric(
    "het<-", signature = c("x", "value"),
    function(x, value)
        standardGeneric("het<-")
)

setGeneric(
    "carrier", signature = "x",
    function(x)
        standardGeneric("carrier")
)

setGeneric(
    "vep", signature = "x",
    function(x)
        standardGeneric("vep")
)

setGeneric(
    "vep<-", signature = c("x", "value"),
    function(x, value)
        standardGeneric("vep<-")
)

setGeneric(
    "bp", signature = "x",
    function(x)
        standardGeneric("bp")
)

setGeneric(
    "bp<-", signature = c("x", "value"),
    function(x, value)
        standardGeneric("bp<-")
)

setGeneric(
    "suffix", signature = "x",
    function(x)
        standardGeneric("suffix")
)

setGeneric(
    "svp", signature = "x",
    function(x)
        standardGeneric("svp")
)

setGeneric(
    "svp<-", signature = c("x", "value"),
    function(x, value)
        standardGeneric("svp<-")
)

# ensemblVEP ----

setGeneric("parseCSQToGRanges", signature = "x",
  function(x, VCFRowID=TRUE, ...)
    standardGeneric("parseCSQToGRanges")
)