Question: how to exclude set of genes from a txdb
0
gravatar for tarek.mohamed
17 months ago by
tarek.mohamed180
tarek.mohamed180 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 • 687 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by tarek.mohamed180

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

ADD REPLYlink written 17 months ago by Santosh Anand3.9k

what is a 'txdb' object ?

ADD REPLYlink written 17 months ago by Pierre Lindenbaum112k

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 17 months ago by Pierre Lindenbaum112k • written 17 months ago by tarek.mohamed180

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 17 months ago by Santosh Anand3.9k
1
gravatar for Santosh Anand
17 months ago by
Santosh Anand3.9k
Santosh Anand3.9k 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 17 months ago by Santosh Anand3.9k

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 17 months ago by tarek.mohamed180

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 17 months ago by Santosh Anand3.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 729 users visited in the last hour