hello, could I ask you a question about targetScan DB. How can I get target miRNAs whose PCT > 0.75? >library(targetscan.Hs.eg.db) >target_miRNA_full = mget('204', targetscan.Hs.egTARGETSFULL) I got 10 miRNAs. now I want to get only three of them whose PCT > 0.75: miR-133,miR-9,miR-124/506 thanks Yu [[alternative HTML version deleted]]

Hi Yu, toTable is one answer: library("targetscan.Hs.eg.db") tgTab <- toTable(targetscan.Hs.egTARGETSFULL) dim(tgTab) ##[1] 54979 8 colnames(tgTab) ##[1] "gene_id" "name" "UTR_start" "UTR_end" "MSA_start" ##[6] "MSA_end" "Seed_match" "PCT" ## convert PCT column to numeric sa as to filter tgTab$PCT[tgTab$PCT == "NULL"] <- NA tgTab$PCT <- as.numeric(tgTab$PCT) tgTab[which(tgTab$gene_id == "204" & tgTab$PCT > 0.75), ] ## gene_id name UTR_start UTR_end MSA_start MSA_end Seed_match PCT ##1461 204 miR-133 854 860 1231 1237 1a 0.8756 ##1462 204 miR-9 761 767 1101 1107 1a 0.8536 ##1467 204 miR-124/506 839 845 1212 1218 m8 0.9485 Best, J. On 06/17/2010 08:37 AM, Yuan Jian wrote: > hello, > > could I ask you a question about targetScan DB. > How can I get target miRNAs whose PCT> 0.75? > >> library(targetscan.Hs.eg.db) >> target_miRNA_full = mget('204', targetscan.Hs.egTARGETSFULL) > I got 10 miRNAs. > now I want to get only three of them whose PCT> 0.75: miR-133,miR-9,miR-124/506 > > thanks > Yu > > > > [[alternative HTML version deleted]] > > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor