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### -------------------------------------------------------------------------
### predictCoding
###
setGeneric("predictCoding",
signature=c("query", "subject", "seqSource", "varAllele"),
function(query, subject, seqSource, varAllele, ...)
standardGeneric("predictCoding")
)
setGeneric("refLocsToLocalLocs",
signature = c("ranges", "txdb", "cdsbytx"),
function(ranges, txdb, cdsbytx, ...)
standardGeneric("refLocsToLocalLocs")
)
setGeneric("getTranscriptSeqs", signature = c("query", "subject"),
function(query, subject, ...)
standardGeneric("getTranscriptSeqs")
)
### -------------------------------------------------------------------------
### locateVariants
###
setGeneric("locateVariants", signature = c("query", "subject", "region"),
function(query, subject, region, ...)
standardGeneric("locateVariants")
)
### -------------------------------------------------------------------------
### summarizeVariants
###
setGeneric("summarizeVariants", signature = c("query", "subject", "mode"),
function(query, subject, mode, ...)
standardGeneric("summarizeVariants")
)
### -------------------------------------------------------------------------
### VariantRegion classes
###
setGeneric("upstream", signature = "x",
function(x) standardGeneric("upstream")
)
setGeneric("upstream<-", signature = "x",
function(x, value) standardGeneric("upstream<-")
)
setGeneric("downstream", signature = "x",
function(x) standardGeneric("downstream")
)
setGeneric("downstream<-", signature = "x",
function(x, value) standardGeneric("downstream<-")
)
### -------------------------------------------------------------------------
### read/write Vcf
###
setGeneric("readVcf", signature = c("file", "genome", "param"),
function(file, genome, param, ...)
standardGeneric("readVcf")
)
setGeneric("readVcfLongForm", signature = c("file", "genome", "param"),
function(file, genome, param, ...)
standardGeneric("readVcfLongForm")
)
setGeneric("writeVcf", signature = c("obj", "filename"),
function(obj, filename, ...)
standardGeneric("writeVcf")
)
### -------------------------------------------------------------------------
### scanVcf
###
setGeneric("ScanVcfParam", signature = "which",
function(fixed=character(), info=character(), geno=character(),
trimEmpty=TRUE, which, ...)
standardGeneric("ScanVcfParam")
)
setGeneric("scanVcfHeader", signature = "file",
function(file, ...) standardGeneric("scanVcfHeader")
)
setGeneric("scanVcf", signature = c("file", "param"),
function(file, ..., param) standardGeneric("scanVcf")
)
### -------------------------------------------------------------------------
### filterVcf
###
setGeneric("filterVcf", signature = "file",
function(file, genome, destination, ..., verbose = FALSE,
index = FALSE, prefilters = FilterRules(),
filters = FilterRules(), param = ScanVcfParam())
standardGeneric("filterVcf")
)
### -------------------------------------------------------------------------
### VCF class
###
setGeneric("fixed", signature = "x",
function(x) standardGeneric("fixed")
)
setGeneric("fixed<-", signature = c("x", "value"),
function(x, value) standardGeneric("fixed<-")
)
setGeneric("ref", signature = "x",
function(x) standardGeneric("ref")
)
setGeneric("ref<-", signature = c("x", "value"),
function(x, value) standardGeneric("ref<-")
)
setGeneric("alt", signature = "x",
function(x) standardGeneric("alt")
)
setGeneric("alt<-", signature = c("x", "value"),
function(x, value) standardGeneric("alt<-")
)
setGeneric("qual", signature = "x",
function(x) standardGeneric("qual")
)
setGeneric("qual<-", signature = c("x", "value"),
function(x, value) standardGeneric("qual<-")
)
setGeneric("filt", signature = "x",
function(x) standardGeneric("filt")
)
setGeneric("filt<-", signature = c("x", "value"),
function(x, value) standardGeneric("filt<-")
)
setGeneric("info", signature = "x",
function(x) standardGeneric("info")
)
setGeneric("info<-", signature = c("x", "value"),
function(x, value) standardGeneric("info<-")
)
setGeneric("geno", signature = c("x", "i"),
function(x, i, ..., withDimnames=TRUE)
standardGeneric("geno"),
)
setGeneric("geno<-", signature = c("x", "i", "value"),
function(x, i, ..., value)
standardGeneric("geno<-")
)
### -------------------------------------------------------------------------
### VCFHeader class
###
setGeneric("reference", signature = "x",
function(x) standardGeneric("reference"),
)
setGeneric("samples", signature = "x",
function(x) standardGeneric("samples"),
)
setGeneric("header", signature = "x",
function(x) standardGeneric("header"),
)
setGeneric("contig", signature = "x",
function(x) standardGeneric("contig"),
)
setGeneric("meta", signature = "x",
function(x) standardGeneric("meta"),
)
### -------------------------------------------------------------------------
### snp encoding methods
###
setGeneric("MatrixToSnpMatrix", signature = c("callMatrix", "ref", "alt"),
function(callMatrix, ref, alt, ...)
standardGeneric("MatrixToSnpMatrix")
)
setGeneric("genotypeToSnpMatrix", signature = "x",
function(x, ...)
standardGeneric("genotypeToSnpMatrix")
)
setGeneric("snpSummary", function(x, ...) standardGeneric("snpSummary") )
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