Question: how to exclude set of genes from a txdb
0
gravatar for tarek.mohamed
3.2 years ago by
tarek.mohamed260
tarek.mohamed260 wrote:

Hi All,

How can I exclude single gene or a list of genes from a txdb object. I have a txdb from hg38 build and I want to exclude single transcript ""uc021wui.2". I can select this transcript using select function from genomic features package. however I do not know how to exclude it from the TxDb object.

library("TxDb.Hsapiens.UCSC.hg38.knownGene") library("org.Hs.eg.db") library("GenomicFeatures") txdb<-(TxDb.Hsapiens.UCSC.hg38.knownGene,miRBaseBuild= "GRCh37.p5") target<-"uc021wui.2" select(txdb,keys=target,keytype = "TXNAME",columns =cols )

Thanks Tarek

txdb • 1.6k views
ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by tarek.mohamed260

what have you tried so far? How did you obtain the txdb object?

ADD REPLYlink written 3.2 years ago by Santosh Anand5.1k

what is a 'txdb' object ?

ADD REPLYlink written 3.2 years ago by Pierre Lindenbaum129k

Hi,

Thanks for the reply I have a txdb from hg38 build and I want to exclude single transcript ""uc021wui.2". I can select this transcript using select function from genomic features package. however I do not know how to exclude it from the TxDb object.

>library("TxDb.Hsapiens.UCSC.hg38.knownGene")
>library("org.Hs.eg.db")
>library("GenomicFeatures")
>txdb<-(TxDb.Hsapiens.UCSC.hg38.knownGene,miRBaseBuild= "GRCh37.p5")
>target<-"uc021wui.2"
>select(txdb,keys=target,keytype = "TXNAME",columns =cols )
ADD REPLYlink modified 3.2 years ago by Pierre Lindenbaum129k • written 3.2 years ago by tarek.mohamed260

Move this comment to question please. Also add an EDIT tag so that users will know that it was added after the Q was published

ADD REPLYlink written 3.2 years ago by Santosh Anand5.1k
1
gravatar for Santosh Anand
3.2 years ago by
Santosh Anand5.1k
Santosh Anand5.1k wrote:

As far as I know, you can select the feature as you have noticed, but can't remove it directly from TxDb. Your options are 1) to create a new TxDb if you need it frequently
https://bioconductor.org/packages/devel/bioc/vignettes/GenomicFeatures/inst/doc/GenomicFeatures.pdf

OR, 2) Just remove that particular gene from the downstream analysis. Where and for what you are using the TxDb downstream?

ADD COMMENTlink written 3.2 years ago by Santosh Anand5.1k

Hi Santosh I am analyzing Chip-seq data, and I am using "chipseeker" package to annotate peaks. For peaks annotation I want to exclude all micro-RNA. I checked the "chipseeker" for such funtion, but I could not find one. So I thought about excluding them from the TxDb file that I use to annotate peaks. ibrary("ChIPseeker") annotatePeak("narrowpeak_bowtie_q0.05_IgG.txt", tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")

ADD REPLYlink written 3.2 years ago by tarek.mohamed260

Hi, I think you are missing something in this line; could you see if this is correct?

txdb<-(TxDb.Hsapiens.UCSC.hg38.knownGene,miRBaseBuild= "GRCh37.p5")

More specifically, I am not sure why "miRBaseBuild" is there and is assigned to a genomeBuild. If possible, repost the main part of the (TxDb related) code again, formatted correctly.

Note: Use the code formatting button (101010) in the markup menu. The one you are using now is for quotation.

ADD REPLYlink written 3.2 years ago by Santosh Anand5.1k
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