Hello,

I have list of transcripts (From an RNA-seq quantification output), and I would like to annotate. I would like the annotation to have the following information (Gene name, NM id or some information about the mRNA, chromosome number, chr start and end)

I tried using the txdb object and sql-like query, but the annotation: (a) only has gene ID and does not have Gene name (b) Its returning multiple rows instead of one row.

Question : Should I be using another hg19 object or another type of query ? Any advice appreciated. 

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene

columns(txdb) #checking what all columns are output
keytypes(txdb)

x=c("uc001aal.1","uc001aaa.3", "uc001aae.4") # example input
cols = columns(txdb)
m = select(txdb, keys = x, columns=cols, keytype="TXNAME") #returns one to many rows

Thanks, K

You should probably be using the Homo.sapiens package, which wraps up a bunch of annotation packages to make this easier. Also, if you just want one row per transcript, you should use mapIds rather than select. Something like this seems appropriate:

> library(Homo.sapiens)
> keys <- keys(Homo.sapiens, "TXNAME")[1:500] ## let's not get crazy here
> colstoget <- c("SYMBOL","ENTREZID","ACCNUM","REFSEQ","TXCHROM","TXSTART","TXEND")
> z1 <- as.data.frame(lapply(colstoget, function(x) mapIds(Homo.sapiens, keys, x, "TXNAME")))
> names(z1) <-  colstoget
> head(z1)
            SYMBOL  ENTREZID   ACCNUM       REFSEQ TXCHROM TXSTART  TXEND
uc001aaa.3 DDX11L1 100287102 AM992871    NR_046018    chr1   11874  14409
uc010nxq.1 DDX11L1 100287102 AM992871    NR_046018    chr1   11874  14409
uc010nxr.1 DDX11L1 100287102 AM992871    NR_046018    chr1   11874  14409
uc001aal.1   OR4F5     79501 BAC05820 NM_001005484    chr1   69091  70008
uc001aaq.2    <NA>      <NA>     <NA>         <NA>    chr1  321084 321115
uc001aar.2    <NA>      <NA>     <NA>         <NA>    chr1  321146 321207

But this only takes the first of any duplicate values, which is sort of naive and stuff. If you can handle ambiguity, you can do something slightly different.

> z2 <- as(lapply(colstoget, function(x) mapIds(Homo.sapiens, keys, x, "TXNAME", multiVals = "CharacterList")), "DataFrame")

> names(z2) <-  colstoget
> z2
DataFrame with 500 rows and 7 columns
                    SYMBOL        ENTREZID
           <CharacterList> <CharacterList>
uc001aaa.3         DDX11L1       100287102
uc010nxq.1         DDX11L1       100287102
uc010nxr.1         DDX11L1       100287102
uc001aal.1           OR4F5           79501
uc001aaq.2              NA              NA
...                    ...             ...
uc001bap.3       ARHGEF10L           55160
uc010ocr.1       ARHGEF10L           55160
uc001baq.3       ARHGEF10L           55160
uc001bar.3       ARHGEF10L           55160
uc010ocs.2       ARHGEF10L           55160
                                           ACCNUM
                                  <CharacterList>
uc001aaa.3         AM992871,BC032353,BC070227,...
uc010nxq.1         AM992871,BC032353,BC070227,...
uc010nxr.1         AM992871,BC032353,BC070227,...
uc001aal.1 BAC05820,NM_001005484,NP_001005484,...
uc001aaq.2                                     NA
...                                           ...
uc001bap.3         AAH65561,AAH80596,AAI17172,...
uc010ocr.1         AAH65561,AAH80596,AAI17172,...
uc001baq.3         AAH65561,AAH80596,AAI17172,...
uc001bar.3         AAH65561,AAH80596,AAI17172,...
uc010ocs.2         AAH65561,AAH80596,AAI17172,...
                                            REFSEQ         TXCHROM
                                   <CharacterList> <CharacterList>
uc001aaa.3                               NR_046018            chr1
uc010nxq.1                               NR_046018            chr1
uc010nxr.1                               NR_046018            chr1
uc001aal.1               NM_001005484,NP_001005484            chr1
uc001aaq.2                                      NA            chr1
...                                            ...             ...
uc001bap.3 NM_001011722,NM_018125,NP_001011722,...            chr1
uc010ocr.1 NM_001011722,NM_018125,NP_001011722,...            chr1
uc001baq.3 NM_001011722,NM_018125,NP_001011722,...            chr1
uc001bar.3 NM_001011722,NM_018125,NP_001011722,...            chr1
uc010ocs.2 NM_001011722,NM_018125,NP_001011722,...            chr1
                   TXSTART           TXEND
           <CharacterList> <CharacterList>
uc001aaa.3           11874           14409
uc010nxq.1           11874           14409
uc010nxr.1           11874           14409
uc001aal.1           69091           70008
uc001aaq.2          321084          321115
...                    ...             ...
uc001bap.3        17907048        18024370
uc010ocr.1        17914911        17966476
uc001baq.3        17941583        18024370
uc001bar.3        17944811        18024370
uc010ocs.2        17944811        18024370

Thank you ! This is great - I will decide what to do about the duplicates.