formatLimmaResult {mi4p} | R Documentation |
Format a Result from Limma
Description
It is not exported by DAPAR
and has to be reproduced here.
Usage
formatLimmaResult(fit, conds, contrast)
Arguments
fit |
Limma fit |
conds |
Condition vector |
contrast |
Contrast vector |
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)
Adapted from the code of Samuel Wieczorek in the DAPAR
package as it is an object that is not exported by the DAPAR
package.
Examples
# library(DAPAR)
set.seed(2016)
data(qData)
data(sTab)
contrast=1
sTab.old <- sTab
conds <- factor(sTab$Condition, levels = unique(sTab$Condition))
sTab <- sTab[unlist(lapply(split(sTab, conds), function(x) {
x["Sample.name"]
})), ]
qData <- qData[, unlist(lapply(split(sTab.old, conds), function(x) {
x["Sample.name"]
}))]
conds <- conds[order(conds)]
res.l <- NULL
design.matrix <- mi4p::make.design(sTab)
contra <- mi4p::make.contrast(design.matrix, condition = conds,
contrast)
cmtx <- limma::makeContrasts(contrasts = contra, levels = make.names(colnames(design.matrix)))
fit <- limma::eBayes(limma::contrasts.fit(limma::lmFit(qData,
design.matrix), cmtx))
res.l <- mi4p::formatLimmaResult(fit, conds, contrast)
[Package mi4p version 1.1 Index]