wrapper.compareNormalizationD_HC: Builds a plot from a dataframe

In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description

#' Wrapper to the function that plot to compare the quantitative proteomics #' data before and after normalization #' #' @title Builds a plot from a dataframe #' #' @param objBefore A dataframe that contains quantitative data before #' normalization. #' #' @param objAfter A dataframe that contains quantitative data after #' normalization. #' #' @param conds A vector of the conditions (one condition per sample). #' #' @param indData2Show A vector of the indices of the columns to show in the #' plot. The indices are those of indices of #' the columns int the data.frame qDataBefore. #' #' @param ... arguments for palette #' #' @return A plot #' #' @author Samuel Wieczorek #' #' @examples #' utils::data(Exp1_R25_pept, package='DAPARdata') #' conds <- Biobase::pData(Exp1_R25_pept)[,"Condition"] #' objAfter <- wrapper.normalizeD(obj=Exp1_R25_pept, method="QuantileCentering",conds = conds, type="within conditions") #' wrapper.compareNormalizationD(Exp1_R25_pept, objAfter, conds) #' #' @importFrom Biobase exprs pData #' #' @export #' #' @importFrom Biobase exprs fData pData #' wrapper.compareNormalizationD <- function(objBefore, objAfter, conds=NULL, indData2Show=NULL, ...)

qDataBefore <- Biobase::exprs(objBefore) qDataAfter <- Biobase::exprs(objAfter) if (is.null(conds)) conds <- Biobase::pData(objBefore)[,"Condition"]

compareNormalizationD(qDataBefore, qDataAfter, conds, indData2Show, ...) Wrapper to the function that plot to compare the quantitative proteomics data before and after normalization.

Usage

wrapper.compareNormalizationD_HC(
  objBefore,
  objAfter,
  condsForLegend = NULL,
  ...
)

Arguments

objBefore	A dataframe that contains quantitative data before normalization.
objAfter	A dataframe that contains quantitative data after normalization.
condsForLegend	A vector of the conditions (one condition per sample).
...	arguments for palette

Value

A plot

Author(s)

Samuel Wieczorek

Examples

utils::data(Exp1_R25_pept, package='DAPARdata')
conds <- Biobase::pData(Exp1_R25_pept)[,"Condition"]
objAfter <- wrapper.normalizeD(obj = Exp1_R25_pept, method = "QuantileCentering",  conds=conds,type = "within conditions")
wrapper.compareNormalizationD_HC(Exp1_R25_pept, objAfter, conds)

DAPAR documentation built on April 11, 2021, 6 p.m.