cwarden45/cohcap

R package for DNA Methylation Analysis (and Gene Expression Integration) for Illumina Infinium Array and BS-Seq Data

COHCAP: R package for DNA Methylation Analysis (and Gene Expression Integration) for Illumina Infinium Array and BS-Seq Data

+ The COHCAP package was first developed within the Bioinformatics Core, under the direction of Yate-Ching Yuan.
+ Charles Warden also provided assistance with updates and maintance that include a Bioconductor version of the package
+ while working in the Integrative Genomics Core (with Xiwei Wu as the director) as well as when he was/is not working at City of Hope.
+
+ Accordingly, Charles Warden, Yate-Ching Yuan, and Xiwei Wu were listed as authors (when a Bioconductor version was available). 

You can directly install from this location using devtools:

If you haven't already installed devtools, you can install the package from CRAN using install.packages("devtools"). Once installed, you can run the following commands:

library("devtools")
devtools::install_github("cwarden45/COHCAP")

Publications

Warden et al. 2013 - original publication; not to be confused with citation for corrigendum in 2019.

Warden 2014 - Bioconductor version (most closely related to this code).

Additional Tutorials (including Post-2016 Updates)

COHCAP Demo for Illumina EPIC Array

Additional Acknowledgements

For Post-2016 function additions / updates, we would like to acknowledge:
- Yuan Yuan MD/PhD for having a project used for initial EPIC testing in the standalone version (which also caused me to debug the custom annotation function in COHCAP).
- Susan Neuhausen / Ding Yuan Chun for projects that led to the addition of continuous variable linear regression analysis.
- Yapeng Su (Caltech, at time of support) for having a project to test application of COHCAP to RRBS data
- D. Joe Jerry (UMass-Amherst) for a project that was helpful for general debugging.
- Feng Miao for having a project where I wrote partially similar code to the COHCAP de novo region boundaries for a 3C-Seq dataset (from the Natarajan Lab)
- Shiuan Chen (application to EPIC dataset, collaboration with Susan Neuhausen)

cohcap's Issues

Troubleshooting Analysis of Heterogenous Patient Data (such as TCGA)

I am transferring part of a discussion from SourceForge to GitHub.

So, I hope it is OK that I am copying the following content, and I will post responses as an individual (truely myself)

Copied (and Slightly Modified) Content

[The] Sample file has only 2 groups i,e primary and solid tisssue normal.

Now the code is :

dir = "/Users/dkaur/Desktop/HNSC/COHCAP/Files"
beta.file = file.path(dir,"S3.txt")
sample.file = file.path(dir,"Sample_HNSC.txt")
expression.file = file.path(dir,"expression-Average_by_Island.txt")
project.folder = "/Users/dkaur/Desktop/HNSC/"
project.name = "HNSC-SUB"

#code chunk number 2: annotation
beta.table = COHCAP.annotate(beta.file, project.name, project.folder,
platform="450k-UCSC")

#code chunk number 3: site
filtered.sites = COHCAP.site(sample.file, beta.table, project.name,
project.folder, ref="Solid Tissue Normal")

#code chunk number 4: island
island.list = COHCAP.avg.by.island(sample.file, filtered.sites, beta.table,
project.name, project.folder, ref="Solid Tissue Normal")

#code chunk number 5: integrate
COHCAP.integrate.avg.by.island(island.list, project.name, project.folder,
expression.file, sample.file)

But i am getting this for my subsample :

"Reading Sample Description File...."
[1] 21 580
[1] 21 578
[1] "Group: Primary.Tumor" "Group: Solid.Tissue.Normal"
[1] "Checking CpG Site Stats Table"
[1] 0 10
[1] 0 10
[1] 0
[1] "Average CpG Sites per CpG Island"
[1] "Differential Methylation Stats for 2 Groups with Reference"
[1] 0 8
[1] 0 8
[1] "There are 0 differentially methylated islands"
[1] 0 580
[1] 0 580

This on my full data :

1] 375044 581
[1] 374979 5
[1] 374979 585
[1] "Reading Sample Description File...."
[1] 374979 580
[1] 374979 578
[1] "Differential Methylation Stats for 2 Groups with Reference"
[1] 374979 5
[1] 374979 10
[1] 374979 10
[1] 0 10
[1] 0 10
[1] "Reading Sample Description File...."
[1] 374979 580
[1] 374979 578
[1] "Group: Primary.Tumor" "Group: Solid.Tissue.Normal"
[1] "Checking CpG Site Stats Table"
[1] 0 10
[1] 0 10
[1] 0
[1] "Average CpG Sites per CpG Island"
[1] "Differential Methylation Stats for 2 Groups with Reference"
[1] 0 8
[1] 0 8
[1] "There are 0 differentially methylated islands"
[1] 0 580
[1] 0 580
[1] 0 580
[1] 0 8
[1] 0

So it seems like there is no differentially methylated sites, which is bit weird. Can you suggest any change in the cutoff values?

what mean HCT116_truncated.bed file?

Hello.

I run COHCAP used manual dataset.
As run that data, I run COHCAP.BSSeq.preprocess command.
I think, BSseq files is exp file, and HCT116 is control file, is that correct?
if HCT116 file is control file, what means each column in HCT116 file? and how can get that file?

Thanks.

Question About Statistical Assumptions

I am paraphrasing an e-mail that I received (and providing this link as a response).

If the sender is OK with it, then I will upload more specific / complete information about question.

Basically, I thought this might be the relevant information:

• Using 0.3 as both methylated and unmethylated threshold
• Reviewer concern that the data is not binomial.

Apology to COHCAP user sending me e-mail

First, I want to apologize to somebody that I will hope tries to contact me again:

An e-mail about a COHCAP error got flagged as spam. Before I realized what I did, I permanently deleted my spam (even though I don't think this was spam). So, if you sent me a message on 2/14/2019, and I never replied, I am very sorry!

Second, since I am making a public apology, I thought maybe this would be a good chance for me to also and maximize exposure to the COHCAP Discussion Group:

https://sourceforge.net/p/cohcap/discussion/bioconductor/

If you do send me an e-mail, I will respond, but I will tell you that you are supposed to post your questions in that discussion group (so that you can learn from other people's questions).

If you post something here, I won't ignore it, but there are not currently any issues posted here. So, to benefit from other questions, I would recommend starting at the other discussion group.

Also, since this "issue" is being posted by the developer, I am intentionally not closing the issue :)