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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.
Examples
library(SummarizedExperiment)
data(Exp1_R25_prot, package='DaparToolshedData')
obj <- Exp1_R25_prot[seq(100)]
level <- 'protein'
metacell.mask <- match.metacell(omXplore::get_metacell(obj[[1]]),
c("Missing POV", "Missing MEC"), level)
# Simulate imputation
assay(obj[[1]])[which(is.na(assay(obj[[1]])))] <- 0
assay(obj[[2]])[which(is.na(assay(obj[[2]])))] <- 0
qData <- as.matrix(SummarizedExperiment::assay(obj[[2]]))
sTab <- SummarizedExperiment::colData(obj)
limma <- limmaCompleteTest(qData, sTab)