# inference for mouse
ppi.infer.mouse <- function (target, kernel, top = 10, classifier = net.infer,
input = "mgi_symbol", output = "mgi_symbol", ...)
{
ensembl <- useMart("ensembl")
mouse.ensembl <- useDataset("mmusculus_gene_ensembl", mart = ensembl)
# input
new.list <- getBM(attributes = c("ensembl_peptide_id", input),
filters = input, values = target, mart = mouse.ensembl)[,1]
new.list <- na.omit(new.list)
# main
ppi.pred.10090 <- classifier(new.list, kernel, ...)
# output
protein_score <- data.frame(ppi.pred.10090$top, ppi.pred.10090$score)
format.protein <- getBM(attributes = c("ensembl_peptide_id", output),
filters = "ensembl_peptide_id", values = ppi.pred.10090$top,
mart = mouse.ensembl)
index <- match(protein_score[, 1], format.protein[, 1])
new.protein_score <- cbind(protein_score, format.protein[index, 2])
new.protein_score[new.protein_score == ""] <- NA
na.omit.new.protein_score <- na.omit(new.protein_score)
ppi.pred.10090$top <- as.vector(na.omit.new.protein_score[1:top, 3])
ppi.pred.10090$score <- as.numeric(na.omit.new.protein_score[1:top, 2])
ppi.pred.10090
}
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