This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Method Article
COHCAP Analysis of CpG Island Methylation for Illumina 450k Methylation Arrays
Charles Warden
Bioinformatics Core, City of Hope Medical Center
Corresponding Author
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
This protocol provides detailed instructions on how to produce quality control metrics, differentially methylated CpG sites, and differentially methylated CpG islands for Illumina 450k methylation array data using the COHCAP Bioconductor package. Scripts for comparing tools to identify differentially methylated regions are also provided, with benchmarks described in the introduction to this protocol.
Keywords
450k array, CpG Islands, COHCAP
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
Charles Warden
commented on 14 April, 2014
COHCAP is now available as a release package:http://bioconductor.org/packages/release/bioc/html/COHCAP.htmlSo, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).
Charles Warden
commented on 27 August, 2014
I have recently learned about this more broad 450k tutorial: https://www.biostars.org/p/110887/Also, these scripts may be worth checking out (but I haven't tried them myself): https://www.biostars.org/p/54994/
Charles Warden
ORCiDcommented on 02 April, 2019
I had to list one group, and COHCAP was originally developed when I was working in the Bioinformatics Core; however, I was actually working in the Integrative Genomics Core when I created the Bioconductor version. That is why I have added Xiwei Wu as an author on the Bioconductor page.
Charles Warden
commented on 14 April, 2014
COHCAP is now available as a release package:http://bioconductor.org/packages/release/bioc/html/COHCAP.htmlSo, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).
Charles Warden
commented on 27 August, 2014
I have recently learned about this more broad 450k tutorial: https://www.biostars.org/p/110887/Also, these scripts may be worth checking out (but I haven't tried them myself): https://www.biostars.org/p/54994/
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 30 Jan, 2014
Community comments: 5
Metrics
Comments: 5
HTML Views: ...
Learn more about our company.
This is a preprint. It has not completed peer review.
Method Article
COHCAP Analysis of CpG Island Methylation for Illumina 450k Methylation Arrays
Charles Warden
Bioinformatics Core, City of Hope Medical Center
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 30 Jan, 2014
Community comments: 5
Metrics
Comments: 5
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
This protocol provides detailed instructions on how to produce quality control metrics, differentially methylated CpG sites, and differentially methylated CpG islands for Illumina 450k methylation array data using the COHCAP Bioconductor package. Scripts for comparing tools to identify differentially methylated regions are also provided, with benchmarks described in the introduction to this protocol.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
Figure 9
Figure 10
Charles Warden
commented on 14 April, 2014
COHCAP is now available as a release package:http://bioconductor.org/packages/release/bioc/html/COHCAP.htmlSo, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).
Charles Warden
commented on 27 August, 2014
I have recently learned about this more broad 450k tutorial: https://www.biostars.org/p/110887/Also, these scripts may be worth checking out (but I haven't tried them myself): https://www.biostars.org/p/54994/
Charles Warden
ORCiDcommented on 02 April, 2019
I had to list one group, and COHCAP was originally developed when I was working in the Bioinformatics Core; however, I was actually working in the Integrative Genomics Core when I created the Bioconductor version. That is why I have added Xiwei Wu as an author on the Bioconductor page.
Charles Warden
commented on 14 April, 2014
COHCAP is now available as a release package:http://bioconductor.org/packages/release/bioc/html/COHCAP.htmlSo, you can now use the standard Bioconductor installation procedure to install COHCAP. Just make sure you are using R-3.1.0 or later (earlier versions of R won't work with Bioconductor 2.14, which is necessary to access the release version of COHCAP).
Charles Warden
commented on 27 August, 2014
I have recently learned about this more broad 450k tutorial: https://www.biostars.org/p/110887/Also, these scripts may be worth checking out (but I haven't tried them myself): https://www.biostars.org/p/54994/