118 lines
3.4 KiB
R
118 lines
3.4 KiB
R
#' @include 02_class_metabarcoding.data.R
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NULL
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# TODO: Add comment
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#
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# Author: coissac
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###############################################################################
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#' @export
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setGeneric("extracts.obiclean", function(obj) {
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return(standardGeneric("extracts.obiclean"))
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})
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#' Extracts the obiclean results
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#'
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#' The method \code{extracts.obiclean} of the class \code{\linkS4class{metabarcoding.data}}
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#' extracts \code{obiclean} results from the MOTUs descriptions include in the
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#' \code{\linkS4class{metabarcoding.data}} instance.
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#' When an \code{obitab} file is imported using the \code{\link{import.metabarcoding.data}}
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#' if \code{obiclean} results are present in the file they are stored in the
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#' \code{motu} data.frame. By calling this methods, MOTU descriptors describing
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#' the \code{obiclean} status are moved to a set of layers.
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#'
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#' @param obj the \code{\linkS4class{metabarcoding.data}} to analyze
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#'
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#' @return the modified \code{\linkS4class{metabarcoding.data}} instance
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#'
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#' @examples
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#'
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#' # load termite data set from the ROBITools sample data
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#' data(termes)
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#'
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#' # shows the initial list of layer names
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#' layer.names(t)
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#'
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#' # extracts the obiclean status
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#' termes = extracts.obiclean(termes)
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#'
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#' # shows the name of the newly created layers
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#' layer.names(t)
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#'
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#'
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#'
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#' @seealso \code{\linkS4class{metabarcoding.data}}, \code{\link{threshold.mask}}, \code{\link{normalize}}
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#'
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#' @docType methods
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#' @rdname extracts-obiclean-methods
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#' @aliases extracts.obiclean-methods,metabarcoding.data
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#' @author Eric Coissac
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#'
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setMethod("extracts.obiclean", "metabarcoding.data", function(obj) {
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pat = "^obiclean_status:.*$"
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cols = colnames(obj@motus)
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cleancols = grep(pat,cols)
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clean.names=cols[cleancols]
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p = grep(pat,cols)
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d = t(as.factor.or.matrix(obj@motus[,p]))
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n = sapply(strsplit(cols[p],':'),function(y) y[[2]])
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rownames(d)=n
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d = d[rownames(obj@reads),]
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obj[["obiclean_status"]]=d
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newmotus = obj@motus[-cleancols]
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pat = "^obiclean_count:.*$"
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cols = colnames(newmotus)
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cleancols = grep(pat,cols)
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clean.names=cols[cleancols]
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p = grep(pat,cols)
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d = t(as.factor.or.matrix(newmotus[,p]))
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n = sapply(strsplit(cols[p],':'),function(y) y[[2]])
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rownames(d)=n
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d = d[rownames(obj@reads),]
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obj[["obiclean_count"]]=d
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newmotus = newmotus[-cleancols]
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pat = "^obiclean_cluster:.*$"
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cols = colnames(newmotus)
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cleancols = grep(pat,cols)
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clean.names=cols[cleancols]
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p = grep(pat,cols)
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d = t(as.factor.or.matrix(newmotus[,p]))
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n = sapply(strsplit(cols[p],':'),function(y) y[[2]])
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rownames(d)=n
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d = d[rownames(obj@reads),]
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obj[["obiclean_cluster"]]=d
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newmotus = newmotus[-cleancols]
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newdata = copy.metabarcoding.data(obj,motus=newmotus)
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return(newdata)
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})
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#' @export
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setGeneric("extracts.obiclean_cluster", function(obj) {
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return(standardGeneric("extracts.obiclean_cluster"))
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})
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setMethod("extracts.obiclean_cluster", "metabarcoding.data", function(obj) {
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obiclean = extracts.obiclean(obj)
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obihead = obiclean[,! is.na(obiclean$motus$obiclean_head)]
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obihead$obiclean_count[is.na(obihead$obiclean_count)]=0
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reads = obihead$obiclean_count
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l = obihead@layers[layer.names(obihead) != "obiclean_count"]
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newdata = copy.metabarcoding.data(obihead,reads=reads,layers=l)
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return(newdata)
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}
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) |