#' These functions will be deprecated. Please use other functions instead.
#'
#' @param x A
#' \code{\link[SummarizedExperiment:SummarizedExperiment-class]{SummarizedExperiment}}
#' object.
#' @param value a matrix to store as the \sQuote{relabundance} assay
#'
#' @param ... Additional parameters. See dedicated function.
#'
#' @name deprecate
NULL
#' @rdname deprecate
#' @export
setGeneric("cluster", signature = c("x"),
function(x,...)
standardGeneric("cluster"))
#' @rdname deprecate
#' @export
setMethod("cluster", signature = c(x = "SummarizedExperiment"),
function(x,...){
.Deprecated(msg = paste0("'cluster' is deprecated. ",
"Use 'addCluster' instead."))
addCluster(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric("addTaxonomyTree",
signature = "x",
function(x, ...)
standardGeneric("addTaxonomyTree"))
#' @rdname deprecate
#' @export
setMethod("addTaxonomyTree", signature = c(x = "SummarizedExperiment"),
function(x,...){
.Deprecated(msg = paste0("'addTaxonomyTree' is deprecated. ",
"Use 'addHierarchyTree' instead."))
addHierarchyTree(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric("taxonomyTree",
signature = "x",
function(x, ...)
standardGeneric("taxonomyTree"))
#' @rdname deprecate
#' @export
setMethod("taxonomyTree", signature = c(x = "SummarizedExperiment"),
function(x,...){
.Deprecated(msg = paste0("'taxonomyTree' is deprecated. ",
"Use 'getHierarchyTree' instead."))
getHierarchyTree(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric("mergeRows",
signature = "x",
function(x, ...)
standardGeneric("mergeRows"))
#' @rdname deprecate
#' @export
setMethod("mergeRows", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeRows' is deprecated. ",
"Use 'agglomerateByVariable' with ",
"parameter by = 'rows' instead."))
agglomerateByVariable(x, by = "rows", ...)
}
)
#' @rdname deprecate
#' @export
setMethod("mergeRows", signature = c(x = "TreeSummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeRows' is deprecated. ",
"Use 'agglomerateByVariable' with ",
"parameter by = 'rows' instead."))
agglomerateByVariable(x, by = "rows", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("mergeCols",
signature = "x",
function(x, ...)
standardGeneric("mergeCols"))
#' @rdname deprecate
#' @export
setMethod("mergeCols", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeCols' is deprecated. ",
"Use 'agglomerateByVariable' with ",
"parameter by = 'cols' instead."))
agglomerateByVariable(x, by = "cols", ...)
}
)
#' @rdname deprecate
#' @export
setMethod("mergeCols", signature = c(x = "TreeSummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeCols' is deprecated. ",
"Use 'agglomerateByVariable' with ",
"parameter by = 'cols' instead."))
agglomerateByVariable(x, by = "cols", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("mergeFeatures",
signature = "x",
function(x, ...)
standardGeneric("mergeFeatures"))
#' @rdname deprecate
#' @export
setMethod("mergeFeatures", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeFeatures' is deprecated. ",
"Use 'agglomerateByVariable' with ",
"parameter by = 'rows' instead."))
agglomerateByVariable(x, by = "rows", ...)
}
)
#' @rdname deprecate
#' @export
setMethod("mergeFeatures", signature = c(x = "TreeSummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeFeatures' is deprecated. ",
"Use 'agglomerateByVariable' with ",
"parameter by = 'rows' instead."))
agglomerateByVariable(x, by = "rows", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("mergeSamples",
signature = "x",
function(x, ...)
standardGeneric("mergeSamples"))
#' @rdname deprecate
#' @export
setMethod("mergeSamples", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeSamples' is deprecated. ",
"Use 'agglomerateByVariable' with ",
"parameter by = 'cols' instead."))
agglomerateByVariable(x, by = "cols", ...)
}
)
#' @rdname deprecate
#' @export
setMethod("mergeSamples", signature = c(x = "TreeSummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeSamples' is deprecated. ",
"Use 'agglomerateByVariable' with ",
"parameter by = 'cols' instead."))
agglomerateByVariable(x, by = "cols", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("mergeFeaturesByRank",
signature = "x",
function(x, ...)
standardGeneric("mergeFeaturesByRank"))
#' @rdname deprecate
#' @export
setMethod("mergeFeaturesByRank", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeFeaturesByRank' is deprecated. ",
"Use 'agglomerateByRank' instead."))
x <- agglomerateByRank(x, ...)
x
}
)
#' @rdname deprecate
#' @export
setMethod("mergeFeaturesByRank", signature = c(x = "SingleCellExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeFeaturesByRank' is deprecated. ",
"Use 'agglomerateByRank' instead."))
x <- agglomerateByRank(x, ...)
x
}
)
#' @rdname deprecate
#' @export
setGeneric("mergeFeaturesByPrevalence", signature = "x",
function(x, ...)
standardGeneric("mergeFeaturesByPrevalence"))
#' @rdname deprecate
#' @export
setMethod("mergeFeaturesByPrevalence", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0(
"'mergeFeaturesByPrevalence' is deprecated. ",
"Use agglomerateByPrevalence instead."))
x <- agglomerateByPrevalence(x, ...)
x
}
)
#' @rdname deprecate
#' @export
setGeneric("getExperimentCrossAssociation", signature = c("x"),
function(x, ...)
standardGeneric("getExperimentCrossAssociation"))
#' @rdname deprecate
#' @export
setMethod("getExperimentCrossAssociation",
signature = c(x = "MultiAssayExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'getExperimentCrossAssociation' is ",
"deprecated. Use ",
"'getCrossAssociation' instead."))
getCrossAssociation(x, ...)
}
)
#' @rdname deprecate
#' @export
setMethod("getExperimentCrossAssociation", signature = "SummarizedExperiment",
function(x, ...){
.Deprecated(msg = paste0("'getExperimentCrossAssociation' is ",
"deprecated. Use ",
"'getCrossAssociation' instead."))
getCrossAssociation(x, ...)
}
)
#' @rdname deprecate
#' @export
setMethod("mergeFeaturesByRank", signature = c(x = "TreeSummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'mergeFeaturesByRank' is deprecated. ",
"Use 'agglomerateByRank' instead."))
x <- agglomerateByRank(x, ...)
x
}
)
#' @rdname deprecate
#' @export
setGeneric("testExperimentCrossAssociation", signature = c("x"),
function(x, ...)
standardGeneric("testExperimentCrossAssociation"))
#' @rdname deprecate
#' @export
setMethod("testExperimentCrossAssociation", signature = c(x = "ANY"),
function(x, ...){
.Deprecated(msg = paste0("'testExperimentCrossAssociation' is ",
"deprecated. Use ",
"'getCrossAssociation' instead."))
getCrossAssociation(x, test.signif = TRUE, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("testExperimentCrossCorrelation", signature = c("x"),
function(x, ...)
standardGeneric("testExperimentCrossCorrelation"))
#' @rdname deprecate
#' @export
setMethod("testExperimentCrossCorrelation", signature = c(x = "ANY"),
function(x, ...){
.Deprecated(msg = paste0("'testExperimentCrossCorrelation' is ",
"deprecated. Use ",
"'getCrossAssociation' instead."))
getCrossAssociation(x, test.signif = TRUE, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("getExperimentCrossCorrelation", signature = c("x"),
function(x, ...)
standardGeneric("getExperimentCrossCorrelation"))
#' @rdname deprecate
#' @export
setMethod("getExperimentCrossCorrelation", signature = c(x = "ANY"),
function(x, ...){
.Deprecated(msg = paste0("'getExperimentCrossCorrelation' is ",
"deprecated. Use ",
"'getCrossAssociation' instead."))
getCrossAssociation(x, ...)
}
)
#' @rdname deprecate
#' @export
loadFromBiom <- function(...) {
.Deprecated(msg = paste0("'loadFromBiom' is deprecated.",
" Use 'importBIOM' instead."))
importBIOM(...)
}
#' @rdname deprecate
#' @export
loadFromQIIME2 <- function(...) {
.Deprecated(msg = paste0("'loadFromQIIME2' is deprecated.",
" Use 'importQIIME2' instead."))
importQIIME2(...)
}
#' @rdname deprecate
#' @export
readQZA <- function(...) {
.Deprecated(msg = paste0("'readQZA' is deprecated.",
" Use 'importQZA' instead."))
importQZA(...)
}
#' @rdname deprecate
#' @export
loadFromMothur <- function(...) {
.Deprecated(msg = paste0("'loadFromMothur' is deprecated.",
" Use 'importMothur' instead."))
importMothur(...)
}
#' @rdname deprecate
#' @export
loadFromMetaphlan <- function(...) {
.Deprecated(msg = paste0("'loadFromMetaphlan' is deprecated.",
" Use 'importMetaPhlAn' instead."))
importMetaPhlAn(...)
}
#' @rdname deprecate
#' @export
loadFromHumann <- function(...) {
.Deprecated(msg = paste0("'loadFromHumann' is deprecated.",
" Use 'importHUMAnN' instead."))
importHUMAnN(...)
}
#' @rdname deprecate
#' @export
setGeneric("countDominantFeatures", signature = c("x"),
function(x, ...)
standardGeneric("countDominantFeatures"))
#' @rdname deprecate
#' @export
setMethod("countDominantFeatures", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = "'countDominantFeatures' function is deprecated. ",
"Use 'summarizeDominance' instead.")
summarizeDominance(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"subsetByRareTaxa", signature = c("x"), function(x, ...)
standardGeneric("subsetByRareTaxa"))
#' @rdname deprecate
#' @export
setMethod(
"subsetByRareTaxa", signature = c(x = "ANY"), function(x, ...){
.Deprecated(
msg = "'subsetByRareTaxa' is deprecated. ",
"Use 'subsetByRare' instead.")
subsetByRare(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"subsetByRareFeatures", signature = c("x"), function(x, ...)
standardGeneric("subsetByRareFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"subsetByRareFeatures", signature = c(x = "ANY"), function(x, ...){
.Deprecated(
msg = "'subsetByRareFeatures' is deprecated. ",
"Use 'subsetByRare' instead.")
subsetByRare(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"subsetByPrevalentTaxa", signature = c("x"), function(x, ...)
standardGeneric("subsetByPrevalentTaxa"))
#' @rdname deprecate
#' @export
setMethod(
"subsetByPrevalentTaxa", signature = c(x = "ANY"), function(x, ...){
.Deprecated(
msg = "'subsetByPrevalentTaxa' is deprecated. Use ",
"'subsetByPrevalent' instead.")
subsetByPrevalent(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"subsetByPrevalentFeatures", signature = c("x"), function(x, ...)
standardGeneric("subsetByPrevalentFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"subsetByPrevalentFeatures", signature = c(x = "ANY"), function(x, ...){
.Deprecated(
msg = "'subsetByPrevalentFeatures' is deprecated. Use ",
"'subsetByPrevalent' instead.")
subsetByPrevalent(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("countDominantTaxa", signature = c("x"),
function(x, ...)
standardGeneric("countDominantTaxa"))
#' @rdname deprecate
#' @export
setMethod("countDominantTaxa", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = "'countDominantTaxa' function is deprecated. ",
"Use 'summarizeDominance' instead.")
summarizeDominance(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("full_join", signature = c("x"),
function(x, ...)
standardGeneric("full_join"))
#' @rdname deprecate
#' @export
setMethod("full_join", signature = c(x = "ANY"),
function(x, ...){
.Deprecated(msg = paste0("'full_join' is deprecated. ",
"Use 'mergeSEs' with 'join = full' ",
"instead."))
mergeSEs(x, join = "full", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("inner_join", signature = c("x"),
function(x, ...)
standardGeneric("inner_join"))
#' @rdname deprecate
#' @export
setMethod("inner_join", signature = c(x = "ANY"),
function(x, ...){
.Deprecated(msg = paste0("'inner_join' is deprecated. ",
"Use 'mergeSEs' with 'join = inner' ",
"instead."))
mergeSEs(x, join = "inner", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("left_join", signature = c("x"),
function(x, ...)
standardGeneric("left_join"))
#' @rdname deprecate
#' @export
setMethod("left_join", signature = c(x = "ANY"),
function(x, ...){
.Deprecated(msg = paste0("'left_join' is deprecated. ",
"Use 'mergeSEs' with 'join = left' ",
"instead."))
mergeSEs(x, join = "left", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("right_join", signature = c("x"),
function(x, ...)
standardGeneric("right_join"))
#' @rdname deprecate
#' @export
setMethod("right_join", signature = c(x = "ANY"),
function(x, ...){
.Deprecated(msg = paste0("'right_join' is deprecated. ",
"Use 'mergeSEs' with 'join = right' ",
"instead."))
mergeSEs(x, join = "right", ...)
}
)
#' @rdname deprecate
#' @export
plotNMDS <- function(x, ...){
.Deprecated(msg = paste0("'plotNMDS' is deprecated. ",
"Use 'scater::plotReducedDim' with ",
"dimred = 'NMDS' instead."))
plotReducedDim(x, ncomponents = 2, dimred = "NMDS",...)
}
#' @rdname deprecate
#' @export
setGeneric("estimateDivergence",signature = c("x"),
function(x, ...)
standardGeneric("estimateDivergence"))
#' @rdname deprecate
#' @export
setMethod("estimateDivergence", signature = c(x="SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'estimateDivergence' is deprecated. ",
"Use 'addDivergence' instead."))
addDivergence(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("meltAssay",signature = "x",
function(x, ...)
standardGeneric("meltAssay"))
#' @rdname deprecate
#' @export
setMethod("meltAssay", signature = c(x="SummarizedExperiment"),
function(x, ...){
.Deprecated(msg = paste0("'meltAssay' is deprecated. ",
"Use 'meltSE' instead."))
meltSE(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"transformSamples", signature = c("x"), function(x,...)
standardGeneric("transformSamples"))
#' @rdname deprecate
#' @export
setMethod(
"transformSamples", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(
"'transformSamples' is deprecated. Use 'transformAssay' instead.")
transformAssay(x, MARGIN = "samples", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"ZTransform", signature = c("x"), function(x, ...)
standardGeneric("ZTransform"))
#' @rdname deprecate
#' @export
setMethod(
"ZTransform", signature = c(x = "SummarizedExperiment"), function(x, ...){
.Deprecated(
"'Ztransform' is deprecated. Use 'transformAssay' instead.")
transformAssay(x, method = "standardize", MARGIN = "features", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"relAbundanceCounts", signature = c("x"), function(x, ...)
standardGeneric("relAbundanceCounts"))
#' @rdname deprecate
#' @export
setMethod(
"relAbundanceCounts", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(
"'relAbundanceCounts' is deprecated. ",
"Use 'transformAssay' instead.")
transformAssay(x, method = "relabundance", MARGIN = "samples", ...)
}
)
#' @rdname deprecate
#' @export
transformCounts <- function(x, ...){
.Deprecated(
"'transformCounts' is deprecated. Use 'transformAssay' instead.")
return(transformAssay(x,...))
}
#' @rdname deprecate
#' @export
setGeneric(
"transformFeatures", signature = c("x"), function(x, ...)
standardGeneric("transformFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"transformFeatures", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(
"'transformFeatures' is deprecated. Use 'transformAssay' instead.")
transformAssay(x, MARGIN = "features", ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"getUniqueFeatures", signature = c("x"), function(x, ...)
standardGeneric("getUniqueFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"getUniqueFeatures", signature = c(x = "SummarizedExperiment"),
function(x,...){
.Deprecated(
msg = "'getUniqueFeatures' is deprecated. Use 'getUnique' instead.")
getUnique(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"getUniqueTaxa", signature = c("x"), function(x, ...)
standardGeneric("getUniqueTaxa"))
#' @rdname deprecate
#' @export
setMethod(
"getUniqueTaxa", signature = c(x = "SummarizedExperiment"), function(x,...){
.Deprecated(
msg = "'getUniqueTaxa' is deprecated. Use 'getUnique' instead.")
getUnique(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"getTopFeatures", signature = "x", function(x,...)
standardGeneric("getTopFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"getTopFeatures", signature = c(x = "SummarizedExperiment"),
function(x,...){
.Deprecated(
msg = "'getTopFeatures' is deprecated. Use 'getTop' instead.")
getTop(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"getTopTaxa", signature = "x", function(x,...)
standardGeneric("getTopTaxa"))
#' @rdname deprecate
#' @export
setMethod(
"getTopTaxa", signature = c(x = "SummarizedExperiment"), function(x,...){
.Deprecated(msg = "'getTopTaxa' is deprecated. Use 'getTop' instead.")
getTop(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"getRareFeatures", signature = "x", function(x, ...)
standardGeneric("getRareFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"getRareFeatures", signature = c(x = "ANY"), function(x,...){
.Deprecated(
msg = "'getRareFeatures' is deprecated. Use 'getRare' instead.")
getRare(x,...)
}
)
#' @rdname deprecate
#' @export
setMethod(
"getRareFeatures", signature = c(x = "SummarizedExperiment"),
function(x,...){
.Deprecated(
msg = "'getRareFeatures' is deprecated. Use 'getRare' instead.")
getRare(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"getRareTaxa", signature = "x", function(x, ...)
standardGeneric("getRareTaxa"))
#' @rdname deprecate
#' @export
setMethod(
"getRareTaxa", signature = c(x = "ANY"), function(x,...){
.Deprecated(
msg = "'getRareTaxa' is deprecated. Use 'getRare' instead.")
getRare(x,...)
}
)
#' @rdname deprecate
#' @export
setMethod(
"getRareTaxa", signature = c(x = "SummarizedExperiment"), function(x,...){
.Deprecated(msg = "'getRareTaxa' is deprecated. Use 'getRare' instead.")
getRare(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"getPrevalentFeatures", signature = "x", function(x, ...)
standardGeneric("getPrevalentFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"getPrevalentFeatures", signature = c(x = "ANY"), function(x,...){
.Deprecated(
msg = "'getPrevalentFeatures' is deprecated. ",
"Use 'getPrevalent' instead.")
getPrevalent(x,...)
}
)
#' @rdname deprecate
#' @export
setMethod(
"getPrevalentFeatures", signature = c(x = "SummarizedExperiment"),
function(x,...){
.Deprecated(
msg = "'getPrevalentFeatures' is deprecated. ",
"Use 'getPrevalent' instead.")
getPrevalent(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"getPrevalentTaxa", signature = "x", function(x, ...)
standardGeneric("getPrevalentTaxa"))
#' @rdname deprecate
#' @export
setMethod(
"getPrevalentTaxa", signature = c(x = "ANY"), function(x,...){
.Deprecated(
msg = "'getPrevalentTaxa' is deprecated. ",
"Use 'getPrevalent' instead.")
getPrevalent(x,...)
}
)
#' @rdname deprecate
#' @export
setMethod(
"getPrevalentTaxa", signature = c(x = "SummarizedExperiment"),
function(x,...){
.Deprecated(
msg = "'getPrevalentTaxa' is deprecated. ",
"Use 'getPrevalent' instead.")
getPrevalent(x,...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"subsampleCounts", signature = c("x"), function(x, ...)
standardGeneric("subsampleCounts"))
#' @rdname deprecate
#' @export
setMethod(
"subsampleCounts", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(
msg = "'subsampleCounts' is deprecated. ",
"Use 'rarefyAssay' instead.")
rarefyAssay(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"addPerSampleDominantFeatures", signature = c("x"), function(x, ...)
standardGeneric("addPerSampleDominantFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"addPerSampleDominantFeatures", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(
msg = "'addPerSampleDominantFeatures' is deprecated.",
" Use 'addDominant' instead.")
addDominant(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"addPerSampleDominantTaxa", signature = c("x"), function(x, ...)
standardGeneric("addPerSampleDominantTaxa"))
#' @rdname deprecate
#' @export
setMethod(
"addPerSampleDominantTaxa", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(
msg = "'addPerSampleDominantTaxa' is deprecated. ",
"Use 'addDominant' instead.")
addDominant(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"perSampleDominantFeatures", signature = c("x"), function(x, ...)
standardGeneric("perSampleDominantFeatures"))
#' @rdname deprecate
#' @export
setMethod(
"perSampleDominantFeatures", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(
msg = "'perSampleDominantFeatures' is deprecated. ",
"Use 'getDominant' instead.")
getDominant(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"perSampleDominantTaxa", signature = c("x"), function(x, ...)
standardGeneric("perSampleDominantTaxa"))
#' @rdname deprecate
#' @export
setMethod(
"perSampleDominantTaxa", signature = c(x = "SummarizedExperiment"),
function(x, ...){
.Deprecated(
msg = "'perSampleDominantTaxa' is deprecated. ",
"Use 'getDominant' instead.")
getDominant(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("makePhyloseqFromTreeSE", signature = c("x"),
function(x, ...)
standardGeneric("makePhyloseqFromTreeSE"))
#' @rdname deprecate
#' @export
setMethod("makePhyloseqFromTreeSE", signature = c(x = "SummarizedExperiment"),
function(x){
.Deprecated(msg = paste0(
"'makeTreeSummarizedExperimentFromPhyloseq' is deprecated.",
" Use 'convertFromPhyloseq' instead."))
convertFromPhyloseq(x)
}
)
#' @rdname deprecate
#' @export
setMethod("makePhyloseqFromTreeSE",
signature = c(x = "TreeSummarizedExperiment"),
function(x){
.Deprecated(msg = paste0(
"'makeTreeSummarizedExperimentFromPhyloseq' is deprecated.",
" Use 'convertFromPhyloseq' instead."))
convertFromPhyloseq(x)
}
)
#' @rdname deprecate
#' @export
setGeneric("makePhyloseqFromTreeSummarizedExperiment", signature = c("x"),
function(x)
standardGeneric("makePhyloseqFromTreeSummarizedExperiment"))
#' @rdname deprecate
#' @export
setMethod("makePhyloseqFromTreeSummarizedExperiment", signature = c(x = "ANY"),
function(x){
.Deprecated(msg = paste0(
"'makePhyloseqFromTreeSummarizedExperiment' is deprecated.",
" Use 'convertToPhyloseq' instead."))
convertToPhyloseq(x)
}
)
#' @rdname deprecate
#' @export
setGeneric("makeTreeSummarizedExperimentFromPhyloseq", signature = c("x"),
function(x)
standardGeneric("makeTreeSummarizedExperimentFromPhyloseq"))
#' @rdname deprecate
#' @export
setMethod("makeTreeSummarizedExperimentFromPhyloseq", signature = c(x = "ANY"),
function(x){
.Deprecated(msg = paste0(
"'makeTreeSummarizedExperimentFromPhyloseq' is deprecated.",
" Use 'convertFromPhyloseq' instead."))
convertFromPhyloseq(x)
}
)
#' @rdname deprecate
#' @export
makeTreeSEFromBiom <- function(...){
.Deprecated(msg = paste0(
"'makeTreeSEFromBiom' is deprecated.",
" Use 'convertFromBIOM' instead."))
convertFromBIOM(...)
}
#' @rdname deprecate
#' @export
makeTreeSummarizedExperimentFromBiom <- function(...){
.Deprecated(msg = paste0(
"'makeTreeSummarizedExperimentFromBiom' is deprecated.",
" Use 'convertFromBIOM' instead."))
convertFromBIOM(...)
}
#' @rdname deprecate
#' @export
makeTreeSEFromDADA2 <- function(...) {
.Deprecated(msg = paste0(
"'makeTreeSEFromDADA2' is deprecated.",
" Use 'convertFromDADA2' instead."))
convertFromDADA2(...)
}
#' @rdname deprecate
#' @export
makeTreeSummarizedExperimentFromDADA2 <- function(...) {
.Deprecated(msg = paste0(
"'makeTreeSummarizedExperimentFromDADA2' is deprecated.",
" Use 'convertFromDADA2' instead."))
convertFromDADA2(...)
}
#' @rdname deprecate
#' @export
makeTreeSEFromPhyloseq <- function(x) {
.Deprecated(msg = paste0(
"'makeTreeSEFromPhyloseq' is deprecated.",
" Use 'convertFromPhyloseq' instead."))
convertFromPhyloseq(x)
}
#' @rdname deprecate
#' @export
setGeneric(
"estimateEvenness", signature = c("x"), function(x, ...)
standardGeneric("estimateEvenness"))
#' @rdname deprecate
#' @export
setMethod(
"estimateEvenness", signature = c(x = "ANY"), function(x, ...){
.Deprecated(msg = paste0(
"'estimateEvenness' is deprecated. Use 'addAlpha' instead."))
addAlpha(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"estimateRichness", signature = c("x"),
function(x, ...) standardGeneric("estimateRichness"))
#' @rdname deprecate
#' @export
setMethod(
"estimateRichness", signature = c(x="ANY"),
function(x, ...){
.Deprecated(msg = paste0(
"'estimateRichness' is deprecated. Use 'addAlpha' instead."))
addAlpha(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"estimateDiversity", signature = c("x"),
function(x, ...) standardGeneric("estimateDiversity"))
#' @rdname deprecate
#' @export
setMethod(
"estimateDiversity", signature = c(x = "ANY"), function(x, ...){
.Deprecated(msg = paste0(
"'estimateDiversity' is deprecated. Use 'addAlpha' instead."))
addAlpha(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"estimateFaith", signature = c("x"), function(x, ...)
standardGeneric("estimateFaith"))
#' @rdname deprecate
#' @export
setMethod(
"estimateFaith", signature = c(x="ANY"),
function(x, ...){
.Deprecated(msg = paste0(
"'estimateFaith' is deprecated. Use 'addAlpha' instead."))
addAlpha(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric(
"estimateDominance", signature = c("x"),
function(x, ...) standardGeneric("estimateDominance"))
#' @rdname deprecate
#' @export
setMethod(
"estimateDominance", signature = c(x="ANY"),
function(x, ...){
.Deprecated(msg = paste0(
"'estimateDominance' is deprecated. Use 'addAlpha' instead."))
addAlpha(x, ...)
})
#' @rdname deprecate
#' @export
setGeneric("subsetSamples", signature = "x",
function(x, ...)
standardGeneric("subsetSamples"))
#' @rdname deprecate
#' @export
setGeneric("subsetFeatures", signature = "x",
function(x, ...)
standardGeneric("subsetFeatures"))
#' @rdname deprecate
#' @export
setGeneric("subsetTaxa", signature = "x",
function(x, ...)
standardGeneric("subsetTaxa"))
#' @rdname deprecate
#' @export
setMethod("subsetSamples", signature = "SummarizedExperiment",
function(x, ...){
.Deprecated(msg = paste0("subsetSamples is deprecated. Please ",
"use '[]' for subsetting instead."))
subset_args <- .get_subset_args(x, ...)
x[subset_args$columns,subset_args$rows]
}
)
#' @rdname deprecate
#' @export
setMethod("subsetFeatures", signature = "SummarizedExperiment",
function(x, ...){
.Deprecated(msg = paste0("subsetFeatures is deprecated. Please",
" use '[]' for subsetting instead."))
subset_args <- .get_subset_args(x, ...)
x[subset_args$rows, subset_args$columns]
}
)
#' @rdname deprecate
#' @export
setMethod("subsetTaxa", signature = "SummarizedExperiment",
function(x, ...){
.Deprecated(msg = paste0("subsetFeatures is deprecated. Please",
" use '[]' for subsetting instead."))
subsetFeatures(x, ...)
}
)
#' @rdname deprecate
#' @export
setGeneric("relabundance", signature = c("x"),
function(x, ...) standardGeneric("relabundance"))
#' @rdname deprecate
#' @export
setGeneric("relabundance<-", signature = c("x"),
function(x, value) standardGeneric("relabundance<-"))
#' @rdname deprecate
#' @importFrom SummarizedExperiment assays
#' @export
setMethod("relabundance", signature = c(x = "SummarizedExperiment"),
function(x){
.Deprecated(msg = paste0("'relabundance' is deprecated\n",
"Use 'assay(x, 'relabundance')' instead."))
assays(x)[["relabundance"]]
}
)
#' @rdname deprecate
#' @importFrom SummarizedExperiment assays<-
#' @export
setReplaceMethod("relabundance", signature = c(x = "SummarizedExperiment"),
function(x, value){
.Deprecated(msg = paste0("'relabundance' is deprecated\n",
"Use 'assay(x, 'relabundance')' instead."))
assays(x)[["relabundance"]] <- value
x
}
)
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