R/filteranot.R

In PADOG: Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)

filteranot = function(esetm = NULL, group = NULL, paired = FALSE, block = NULL, annotation = NULL, 
    include.details = FALSE) {
    
    Block = block
    if (! annotation %in% c("hgu133a.db", "hgu133plus2.db")) {
        stopifnot(require(annotation, character.only = TRUE))
    }
    
    if (!paired) {
        G = factor(group)
        design <- model.matrix(~0 + G)
        colnames(design) <- levels(G)
        fit <- lmFit(esetm, design)
        cont.matrix <- makeContrasts(contrasts = "d-c", levels = design)
        fit2 <- contrasts.fit(fit, cont.matrix)
        fit2 <- eBayes(fit2)
        aT1 <- topTable(fit2, coef = 1, number = dim(esetm)[1])
    } else {
        G = group
        block = factor(Block)
        G = factor(G)
        design <- model.matrix(~0 + G + block)
        colnames(design) <- substr(colnames(design), 2, 100)
        fit <- lmFit(esetm, design)
        cont.matrix <- makeContrasts(contrasts = "d-c", levels = design)
        fit2 <- contrasts.fit(fit, cont.matrix)
        fit2 <- eBayes(fit2)
        aT1 <- topTable(fit2, coef = 1, number = dim(esetm)[1])
    }
    # annotate ids to ENTREZID
    aT1$ID = rownames(aT1)
    anpack = paste(unlist(strsplit(annotation, split = ".db")), "ENTREZID", sep = "")
    aT1 <- aT1[aT1$ID %in% keys(get(anpack)), ]
    aT1$ENTREZID = unlist(as.list(get(anpack)[aT1$ID]))
    aT1 <- aT1[!is.na(aT1$ENTREZID), ]
    aT1 <- aT1[!duplicated(aT1$ENTREZID), ]
    
    if (include.details) {
        return(aT1)
    } else {
        return(aT1[, c("ID", "ENTREZID")])
    }
    
}