Open dariader opened 1 year ago
Hello, Can you please help me to find the dictionary that is used in this function? gene-convert-dict.rds
Thanks!
GTExVIPER <- function(dat.mat, gtex.path, num.nets = 3) { ## convert to entrez convert.dict <- readRDS(paste(gtex.path, 'gene-convert-dict.rds', sep = '')) dat.mat <- dat.mat[ which(rownames(dat.mat) %in% convert.dict$Ensembl.Gene.ID) ,] # remove rows with no ENSG match rname.match <- match(rownames(dat.mat), convert.dict$Ensembl.Gene.ID) # match remaining ENSG names entrez.names <- convert.dict$Entrez.Gene.ID[rname.match] # get Entrez names na.inds <- which(is.na(entrez.names)) # remove NA entrez names from matrix dat.mat <- dat.mat[ -na.inds ,]; entrez.names <- entrez.names[ -na.inds] rownames(dat.mat) <- entrez.names print(dim(dat.mat)) ## load in all gtex networks net.files <- dir(gtex.path, pattern = '*.rda') gtex.nets <- list() for (i in 1:length(net.files)) { gtex.nets[[i]] <- get(load( paste(gtex.path, net.files[i], sep = '') )) } ## compute VIPER for all the networks viper.mats <- list() for (i in 1:length(gtex.nets)) { viper.mats[[i]] <- viper(dat.mat, gtex.nets[[i]], method = 'none') } ## identify the most important networks (as defined by num.nets) net.counts <- rep(0, length(gtex.nets)); names(net.counts) <- 1:length(gtex.nets) shared.regs <- Reduce(intersect, lapply(viper.mats, rownames)) for (i in 1:length(shared.regs)) { reg <- shared.regs[i] reg.mat <- as.data.frame(lapply(viper.mats, function(x) { x[reg,] })) max.inds <- apply(reg.mat, 1, function(x) { which.max(abs(x)) } ) for (j in 1:length(max.inds)) { net.counts[ max.inds[j] ] <- net.counts[ max.inds[j] ] + 1 } } net.counts <- sort(net.counts, decreasing = TRUE) top.nets <- as.numeric(names(net.counts)[1:num.nets]) ## clean up for memory purposes rm(viper.mats) ## integrate the results of the three selected networks mVip.mat <- viper(dat.mat, regulon = gtex.nets[top.nets], method = 'none') ## convert to ensemble mVip.mat <- mVip.mat[ which(rownames(mVip.mat) %in% convert.dict$Entrez.Gene.ID) ,] rname.match <- match(rownames(mVip.mat), convert.dict$Entrez.Gene.ID) ensg.names <- convert.dict$Ensembl.Gene.ID[rname.match] na.inds <- which(ensg.names == '') mVip.mat <- mVip.mat[ -na.inds ,]; ensg.names <- ensg.names[ -na.inds ] rownames(mVip.mat) <- ensg.names ## return return(mVip.mat) }
Do you have found the rds file? I have the same question.Thank you!
Hello, Can you please help me to find the dictionary that is used in this function? gene-convert-dict.rds
Thanks!