[BioC] targetscan

[James F. Reid]

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
>
>
>
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