wrapper.impute.slsa {DAPAR}R Documentation

Imputation of peptides having no values in a biological condition.

Description

#' This method replaces each missing value by a given value #' #' @title Deterministic imputation #' #' @param qdata An expression set containing quantitative or missing values #' #' @param metadata xxx #' #' @param values A vector with as many elements as the number of colums #' of qdata #' #' @param na.type xxx #' #' @return An imputed dataset #' #' @author Thomas Burger, Samuel Wieczorek #' #' @examples #' utils::data(Exp1_R25_pept, package='DAPARdata') #' qdata <- Biobase::exprs(Exp1_R25_pept) #' meta <- #' values <- getQuantile4Imp(qdata)$shiftedImpVal #' obj.imp.mec <- impute.detQuant(qdata, values, na.type = 'missing POV') #' obj.imp.mec <- impute.detQuant(qdata, values, na.type = 'missing MEC') #' obj.imp.na <- impute.detQuant(qdata, values, na.type = 'missing') #' #' @export #' impute.detQuant <- function(qdata, metadata, values, na.type=NULL) availablePatterns <- unname(search.metacell.tags(pattern=na.type, level=obj@experimentData@other$typeOfData)) if (is.null(na.type)) stop(paste0("'na.type' is required. Available values are:.", paste0(metacell.def(), collapse=' ')) ) else if (!(na.type level=obj@experimentData@other$typeOfData))) stop(paste0("Available values for na.type are: ", paste0(availablePatterns, collapse=' ')) )

if(missing(metadata)) stop("'metadata' is missing.")

#browser() for(i in 1:ncol(qdata)) col <- qdata[,i] ind.na.type <- match.metacell(Biobase::fData(obj)[, obj@experimentData@other$names_metacell[i]], pattern = na.type, level = obj@experimentData@other$typeOfData)

col[which(is.na(col) & ind.na.type)] <- values[i] qdata[,i] <- col return(qdata)

Usage

wrapper.impute.slsa(obj = NULL, na.type = NULL)

Arguments

obj

An object of class MSnSet.

na.type

A string which indicates the type of missing values to impute. Available values are: 'NA' (for both POV and MEC), 'POV', 'MEC'.

Details

This method is a wrapper to the function impute.slsa of the package imp4p adapted to an object of class MSnSet.

Value

The exprs(obj) matrix with imputed values instead of missing values.

Author(s)

Samuel Wieczorek

Examples

utils::data(Exp1_R25_pept, package='DAPARdata')
obj <- Exp1_R25_pept[1:100]
obj.slsa.pov <- wrapper.impute.slsa(obj, na.type = 'missing POV')


[Package DAPAR version 1.26.0 Index]