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

In prostarproteomics/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

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(100)]
level <- 'protein'
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), 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)

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.