R/siamcat_class_assignment_methods.R

In KonradZych/SIAMCAT: Statistical Inference of Associations between Microbial Communities And host phenoTypes

#!/usr/bin/Rscript
### SIAMCAT - Statistical Inference of Associations between
### Microbial Communities And host phenoTypes R flavor EMBL
### Heidelberg 2012-2018 GNU GPL 3.0

###############################################################################
#' Assign a new phyloseq object to \code{x}
#'
#' @usage physeq(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an object of class \link[phyloseq]{phyloseq-class}
#' @export
#' @docType methods
#' @rdname assign-physeq
#' @aliases assign-physeq
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' physeq(siamcat_example) <- physeq(siamcat_example)
setGeneric("physeq<-", function(x, value)
    standardGeneric("physeq<-"))
#' @rdname assign-physeq
#' @aliases physeq<-
setMethod("physeq<-", c("siamcat", "phyloseq"), function(x, value) {
    siamcat(
        value,
        x@model_list,
        x@eval_data,
        x@label,
        x@norm_param,
        x@data_split,
        x@pred_matrix,
        x@orig_feat
    )
})
#' @rdname assign-physeq
#' @aliases physeq<-
setMethod("physeq<-", c("siamcat", "otu_table"), function(x, value) {
    phyloseq <- physeq(x)
    otu_table(phyloseq) <- value
    siamcat(
        phyloseq,
        x@model_list,
        x@eval_data,
        x@label,
        x@norm_param,
        x@data_split,
        x@pred_matrix,
        x@orig_feat
    )
})


###############################################################################
#' Assign a new label object to \code{x}
#'
#' @usage label(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an object of class \link{label-class}
#' @export
#' @docType methods
#' @rdname assign-label
#' @aliases assign-label
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' label(siamcat_example) <- label(siamcat_example)
setGeneric("label<-", function(x, value)
    standardGeneric("label<-"))
#' @rdname assign-label
#' @aliases label<-
setMethod("label<-", c("siamcat", "label"), function(x, value) {
    siamcat(
        value,
        x@model_list,
        x@eval_data,
        x@phyloseq,
        x@orig_feat,
        x@norm_param,
        x@data_split,
        x@pred_matrix
    )
})


###############################################################################
#' Assign a new model_list object to \code{x}
#'
#' @usage model_list(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an object of class \link{model_list-class}
#' @export
#' @docType methods
#' @rdname assign-model_list
#' @aliases assign-model_list
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' model_list(siamcat_example) <- model_list(siamcat_example)
setGeneric("model_list<-", function(x, value)
    standardGeneric("model_list<-"))
#' @rdname assign-model_list
#' @aliases model_list<-
setMethod("model_list<-", c("siamcat", "model_list"), function(x, value) {
    siamcat(
        value,
        x@label,
        x@eval_data,
        x@phyloseq,
        x@orig_feat,
        x@norm_param,
        x@data_split,
        x@pred_matrix
    )
})

###############################################################################
#' Assign a new eval_data object to \code{x}
#'
#' @usage eval_data(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an eval_data list
#' @export
#' @docType methods
#' @rdname assign-eval_data
#' @aliases assign-eval_data
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' eval_data(siamcat_example) <- eval_data(siamcat_example)
setGeneric("eval_data<-", function(x, value)
    standardGeneric("eval_data<-"))
#' @rdname assign-eval_data
#' @aliases eval_data<-
setMethod("eval_data<-", c("siamcat", "list"), function(x, value) {
    siamcat(
        value,
        x@label,
        x@model_list,
        x@phyloseq,
        x@orig_feat,
        x@norm_param,
        x@data_split,
        x@pred_matrix
    )
})

###############################################################################
#' Assign a new norm_param object to \code{x}
#'
#' @usage norm_param(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an norm_param list
#' @export
#' @docType methods
#' @rdname assign-norm_param
#' @aliases assign-norm_param
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' norm_param(siamcat_example) <- norm_param(siamcat_example)
setGeneric("norm_param<-", function(x, value)
    standardGeneric("norm_param<-"))
#' @rdname assign-norm_param
#' @aliases norm_param<-
setMethod("norm_param<-", c("siamcat", "list"), function(x, value) {
    siamcat(
        value,
        x@label,
        x@model_list,
        x@phyloseq,
        x@orig_feat,
        x@eval_data,
        x@data_split,
        x@pred_matrix
    )
})

###############################################################################
#' Assign a new pred_matrix object to \code{x}
#'
#' @usage pred_matrix(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an pred_matrix matrix
#' @export
#' @docType methods
#' @rdname assign-pred_matrix
#' @aliases assign-pred_matrix
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' pred_matrix(siamcat_example) <- pred_matrix(siamcat_example)
setGeneric("pred_matrix<-", function(x, value)
    standardGeneric("pred_matrix<-"))
#' @rdname assign-pred_matrix
#' @aliases pred_matrix<-
setMethod("pred_matrix<-", c("siamcat", "matrix"), function(x, value) {
    siamcat(
        value,
        x@label,
        x@model_list,
        x@phyloseq,
        x@orig_feat,
        x@eval_data,
        x@data_split,
        x@norm_param
    )
})

###############################################################################
#' Assign a new data_split object to \code{x}
#'
#' @usage data_split(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an object of class \link{data_split-class}
#' @export
#' @docType methods
#' @rdname assign-data_split
#' @aliases assign-data_split
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' data_split(siamcat_example) <- data_split(siamcat_example)
setGeneric("data_split<-", function(x, value)
    standardGeneric("data_split<-"))
#' @rdname assign-data_split
#' @aliases data_split<-
setMethod("data_split<-", c("siamcat", "data_split"), function(x, value) {
    siamcat(
        value,
        x@label,
        x@model_list,
        x@phyloseq,
        x@orig_feat,
        x@eval_data,
        x@pred_matrix,
        x@norm_param
    )
})

###############################################################################
#' Assign a new otu_table object to \code{x} orig_feat slot
#'
#' @usage orig_feat(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an object of class \link[phyloseq]{otu_table-class}
#' @export
#' @docType methods
#' @rdname assign-orig_feat
#' @aliases assign-orig_feat
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' orig_feat(siamcat_example) <- orig_feat(siamcat_example)
setGeneric("orig_feat<-", function(x, value)
    standardGeneric("orig_feat<-"))
#' @rdname assign-orig_feat
#' @aliases orig_feat<-
setMethod("orig_feat<-", c("siamcat", "orig_feat"), function(x, value) {
    siamcat(
        value,
        x@label,
        x@model_list,
        x@phyloseq,
        x@data_split,
        x@eval_data,
        x@pred_matrix,
        x@norm_param
    )
})
#' @rdname assign-orig_feat
#' @aliases orig_feat<-
setMethod("orig_feat<-", c("siamcat", "otu_table"), function(x, value) {
    siamcat(
        new("orig_feat", value),
        x@label,
        x@model_list,
        x@phyloseq,
        x@data_split,
        x@eval_data,
        x@pred_matrix,
        x@norm_param
    )
})


###############################################################################
#' Assign a new otu_table object to \code{x} features slot
#'
#' @usage features(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an object of class \link[phyloseq]{otu_table-class}
#' @export
#' @docType methods
#' @rdname assign-features
#' @aliases assign-features
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' features(siamcat_example) <- features(siamcat_example)
setGeneric("features<-", function(x, value)
    standardGeneric("features<-"))
#' @rdname assign-features
#' @aliases features<-
setMethod("features<-", c("siamcat", "otu_table"), function(x, value) {
    otu_table(physeq(x)) <-  value
    return(x)
})

###############################################################################
#' Assign a new sam_data object to \code{x}
#'
#' @usage meta(x) <- value
#'
#' @param x an object of class \link{siamcat-class}
#' @param value an object of class \link[phyloseq]{sample_data-class}
#' @export
#' @docType methods
#' @rdname assign-meta
#' @aliases assign-meta
#' @return none
#'
#' @examples
#' data(siamcat_example)
#' meta(siamcat_example) <- meta(siamcat_example)
setGeneric("meta<-", function(x, value)
    standardGeneric("meta<-"))
#' @rdname assign-meta
#' @aliases meta<-
setMethod("meta<-", c("siamcat", "sample_data"), function(x, value) {
    sample_data(physeq(x)) <-  value
    return(x)
})