Nothing
######################################################################
########################### Class EnrichSNP ##########################
############################## Creation ##############################
######################################################################
setClass(
Class = "EnrichSNP",
representation = representation(
List = "character",
Table = "matrix",
EnrichmentRatio = "numeric",
Z = "numeric",
PValue = "numeric",
Resampling = "matrix"
),
prototype = prototype(
List = character(),
Table = matrix(0, ncol = 2, nrow = 2),
EnrichmentRatio = numeric(),
Z = numeric(),
PValue = numeric(),
Resampling = matrix(0, ncol = 5, nrow = 0)
)
)
setMethod(f = "enrichSNP", signature = "ANY", definition = function (List, Table, EnrichmentRatio, Z, PValue, Resampling) {
if (missing(List)) {
List <- character()
} else {}
if (missing(Table)) {
Table <- matrix(0, ncol = 2, nrow = 2)
} else {}
if (missing(EnrichmentRatio)) {
EnrichmentRatio <- numeric()
} else {}
if (missing(Z)) {
Z <- numeric()
} else {}
if (missing(PValue)) {
PValue <- numeric()
} else {}
if (missing(Resampling)) {
Resampling <- matrix(0, ncol = 5, nrow = 0)
} else {}
return(new("EnrichSNP", List = List, Table = Table, EnrichmentRatio = EnrichmentRatio, Z = Z, PValue = PValue, Resampling = Resampling))
})
setMethod(f = "is.EnrichSNP", signature = "ANY", definition = function (object) {
if (length(object)>1) {
return(sapply(object, is.EnrichSNP))
} else {
if (class(object) == "EnrichSNP") {
return(TRUE)
} else {
return(FALSE)
}
}
})
setMethod(f = "print", signature = "EnrichSNP", definition = function (x) {
EnrichmentRatio <- eval(parse(text = paste0('x@EnrichmentRatio')))
Z <- eval(parse(text = paste0('x@Z')))
PValue <- eval(parse(text = paste0('x@PValue')))
Resampling <- eval(parse(text = paste0('nrow(x@Resampling)')))
Data <- eval(parse(text = paste0('sum(x@Table)')))
List <- eval(parse(text = paste0('length(x@List)')))
resTmp <- c(if (length(EnrichmentRatio)==0) {NA} else {EnrichmentRatio},
if (length(Z)==0) {NA} else {Z},
if (length(PValue)==0) {NA} else {PValue},
Resampling,
Data,
List
)
names(resTmp) <- c("EnrichmentRatio", "Z", "PVALUE", "nbSample", "SNP", "eSNP")
res <- t(resTmp)
rownames(res) <- "eSNP"
return(res)
})
.EnrichSNP.show <- function (object) {
cat(" - List :",
paste0("(", length(object@List), ")"),
if (length(object@List) <= 5) {
if (length(object@List) == 0) {
"NA"
} else {
object@List
}
} else {
paste(paste(object@List[seq(5)], collapse = " "), "...")
}
)
cat("\n - Table :", paste0("(", paste(dim(object@Table), collapse = "x"), ")"))
if (all(object@Table == 0)) {
cat(" NA")
} else {
cat("\n")
resFormat <- cbind(c("", rownames(object@Table)), rbind(colnames(object@Table), apply(round(object@Table, digits = 4), 2, as.character)))
cat(paste(" ", apply(apply(matrix(paste0(" ", resFormat, " "), nrow = nrow(resFormat)), 2, format, justify = "centre"), 1, paste, collapse = ""), "\n", sep = "", collapse = ""))
}
cat("\n - EnrichmentRatio :", ifelse(length(object@EnrichmentRatio) == 0, NA, object@EnrichmentRatio))
cat("\n - Z :", ifelse(length(object@Z) == 0, NA, object@Z))
cat("\n - PValue :", ifelse(length(object@PValue) == 0, NA, ifelse((object@PValue==0 & nrow(object@Resampling)!=0), paste0("<", 1/nrow(object@Resampling)), object@PValue)))
cat("\n - Resampling :", paste0("(", paste(dim(object@Resampling), collapse = "x"), ")"), ifelse(nrow(object@Resampling) == 0, 0, nrow(object@Resampling)))
cat("\n")
return(invisible(object))
}
setMethod(f = "show", signature = "EnrichSNP", definition = function (object) {cat(" ~~~ Class:", class(object), "~~~\n"); .EnrichSNP.show(object); return(invisible(object))})
setMethod(f = "[", signature = "EnrichSNP", definition = function (x, i, j, drop) {
switch(EXPR = i,
"List" = {return(x@List)},
"Table" = {return(x@Table)},
"EnrichmentRatio" = {return(x@EnrichmentRatio)},
"Z" = {return(x@Z)},
"PValue" = {return(x@PValue)},
"Resampling" = {return(x@Resampling)},
stop('[EnrichSNP:get] ', i, ' is not a "EnrichSNP" slot.', call. = FALSE)
)
})
setMethod(f = "[<-", signature = "EnrichSNP", definition = function (x, i, j, value) {
switch(EXPR = i,
"List" = {x@List <- value},
"Table" = {x@Table <- value},
"EnrichmentRatio" = {x@EnrichmentRatio <- value},
"Z" = {x@Z <- value},
"PValue" = {x@PValue <- value},
"Resampling" = {x@Resampling <- value},
stop('[EnrichSNP:set] ', i, ' is not a "EnrichSNP" slot.', call. = FALSE)
)
validObject(x)
return(x)
})
setMethod(f = "reset", signature = "EnrichSNP", definition = function (object, i) {
switch(EXPR = i,
"List" = {object@List <- character()},
"Table" = {object@Table <- matrix(0, ncol = 2, nrow = 2)},
"EnrichmentRatio" = {object@EnrichmentRatio <- numeric()},
"Z" = {object@Z <- numeric()},
"PValue" = {object@PValue <- numeric()},
"Resampling" = {object@Resampling <- matrix(0, ncol = 5, nrow = 0)},
stop('[EnrichSNP:reset] ', i, ' is not a "EnrichSNP" slot.', call. = FALSE)
)
return(object)
})
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