diffAnaGetSignificant: Returns a MSnSet object with only proteins significant after...

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

Returns a MSnSet object with only proteins significant after differential analysis.

Description

Returns a MSnSet object with only proteins significant after differential analysis.

Usage

diffAnaGetSignificant(obj)

Arguments

obj	An object of class MSnSet.

Value

A MSnSet

Author(s)

Alexia Dorffer

Examples

utils::data(Exp1_R25_prot, package='DAPARdata')
obj <- Exp1_R25_prot[1:1000]
level <- obj@experimentData@other$typeOfData
metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1)
obj <- MetaCellFiltering(obj, indices, cmd='delete')
qData <- Biobase::exprs(obj$new)
sTab <- Biobase::pData(obj$new)
allComp <- limmaCompleteTest(qData,sTab)
data <- list(logFC=allComp$logFC[1], P_Value = allComp$P_Value[1])
obj$new <- diffAnaSave(obj$new, allComp, data)
signif <- diffAnaGetSignificant(obj$new)

samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.