formatLimmaResult: xxxx

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

xxxx

Description

xxxx

Usage

formatLimmaResult(fit, conds, contrast, design.level)

Arguments

fit	xxxx
conds	xxxx
contrast	xxxx
design.level	xxx

Value

A list of two dataframes : logFC and P_Value. The first one contains the logFC values of all the comparisons (one column for one comparison), the second one contains the pvalue of all the comparisons (one column for one comparison). The names of the columns for those two dataframes are identical and correspond to the description of the comparison.

Author(s)

Samuel Wieczorek

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)
limma <- limmaCompleteTest(qData, sTab)

prostarproteomics/DAPAR documentation built on March 28, 2024, 4:44 a.m.