Question: creating custom genome annotation for the ChIPQC package
1
gravatar for Philip Lijnzaad
4.3 years ago by
European Union
Philip Lijnzaad160 wrote:

This is a summary of an e-mail exchange I had with Tom Caroll, about creating custom annotations for the ChIPQC package. Reproduced so that other can make use of it.

Philip Lijnzaad

--------

> Dear Tom and/or Rory,
> I am interested to use your ChIPQC package for our yeast data, but there is no standard yeast annotation that I can use.

On 08/07/2015 11:14 AM, tom carroll wrote:

You can provide your own annotation in the form of a named list of GRanges with the first element of the list containing a character vector of version.
I include an example below.  I did do a course in Boston you may find useful and contains information on custom annotation.http://bioconductor.org/help/course-materials/2014/BioC2014/Bioc2014_ChIPQC_Practical.pdf

##########################################
## You can also provide your own denovo List of GRanges but first
element must be a character with name "version".

library(GenomicRanges)
library(ChIPQC)
customAnnotation <- list(
  version="TomsCustom",
  Test=GRanges("chr19",IRanges(1,10000000)),
  AnotherTest=GRanges("chr19",IRanges(10000000,20000000))
  )
testExp <- ChIPQCsample("ETOH_Rep2.bamRange5.bam",annotation=customAnnotation,chromosomes=c("chr19"))
plotRegi(testExp)
##########

 

chipseq chipqc qc • 1.3k views
ADD COMMENTlink modified 4.3 years ago by Thomas Carroll400 • written 4.3 years ago by Philip Lijnzaad160
Answer: creating custom genome annotation for the ChIPQC package
2
gravatar for Thomas Carroll
4.3 years ago by
United States/New York/The Rockefeller University
Thomas Carroll400 wrote:

hi Philip,

Thanks for posting this here.

You can provide your own annotation in the form of a named list of GRanges with the first element of the list containing a character vector of version.

I include an example below.  I did a course in Boston you may find useful and contains information on custom annotation.

http://bioconductor.org/help/course-materials/2014/BioC2014/Bioc2014_ChIPQC_Practical.pdf

I can look to add a yeast annotation too. As long as we have a suitable TXDB package it should be simple although i am sure one can create our own TXDB for any genome not currently supported.

best,

Tom

 

 

 


##########################################
## You can also provide your own denovo List of GRanges but first
element must be a character with name "version".

library(GenomicRanges)

library(ChIPQC)
customAnnotation <- list(
  version="TomsCustom",
  Test=GRanges("chr19",IRanges(1,10000000)),
  AnotherTest=GRanges("chr19",IRanges(10000000,20000000))
  )
testExp <- ChIPQCsample("ETOH_Rep2.bamRange5.bam",annotation=customAnnotation,chromosomes=c("chr19"))
plotRegi(testExp)
##########

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Thomas Carroll400
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