EpiDISH

[sjczheng]

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• Repository: https://github.com/sjczheng/EpiDISH

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[bioc-issue-bot]

Hi @sjczheng

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: EpiDISH
Title: Epigenetic Dissection of Intra-Sample-Heterogeneity
Version: 0.99.0
Description: EpiDISH is a R package to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.
Date: 2017-06-26
Author: Andrew E. Teschendorff <a.teschendorff@ucl.ac.uk>, Shijie C. Zheng<shijieczheng@gmail.com>
Maintainer: Shijie Charles Zheng<shijieczheng@gmail.com>
Depends: R (>= 3.4), Biobase, MASS, e1071, quadprog
Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
License: GPL-2
LazyData: true
NeedsCompilation: no
Packaged: 2016-11-23 14:27:33 UTC; Charles
RoxygenNote: 6.0.1
URL: https://github.com/sjczheng/EpiDISH
BugReports: https://github.com/sjczheng/EpiDISH/issues
biocViews: DNAMethylation, MethylationArray, Epigenetics 

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "skipped, ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/EpiDISH_buildreport_20170627070026.html

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

6a675a7 fix error

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/EpiDISH_buildreport_20170627083354.html

[dvantwisk]

We've reviewed your package! It looks good, but there are places for improvement.

DESCRIPTION

• L8: Unless the user needs to have access to the symbols in the packages in 'Depends: ', it is best to place these in a section labeled 'Imports: '

NAMESPACE

• Consider explicitly enumerating what symbols are being imported using importFrom() in the roxygen2 header.

R

R/DummyBeta.m.R & R/centDHSblood.m.R

• Needs more description for man pages so a new user can understand what the data sets are.

R/epidish.R

• L94: Better to put argument validation upfront instead of at end of function. Use match.arg().

• L101: Similar to the issue with L94, use match.arg() to validate constraints input. Make 'constraints' in function definition equal to c('inequality', 'equality').

• L124: Consider using seq_len() instead of : in the for-loop. This prevents the edge case where 1:0 results in 0.

• L168-170: Code can be vectorized with:

s <- seq_len(ncol(avdata.m))
rmse.m[s,nui] <- sqrt(colMeans((data2.m[,s] - reconst.m[,s])^2))

• L171: Use message() instead of print. message() will output to stderr as opposed to print() that outputs to stdout.

• L187-192: Vectorize the code. Instead of nested for-loops, replace with:

  D <- apply(ref.m, 2, function(x) colSums(x * ref.m))

• L196-201: Simplify code with:

  A.m <- matrix(1, nrow=ncol(ref.m) + 1, ncol=nW)
  A.m[,1] <- -1

• L194-247: The if and else blocks both have almost the same code. Consider making a private function that performs the task so that code is not repeated.

• Consider using the formatR package for cleaning up indentation in this file.

man

Looks good!

test

[Recommended] Include tests to verify functionality and input handling of the epidish() function. See the testthat package for more information.

vignettes

Looks good!

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

082dcf5 improve and add test

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/EpiDISH_buildreport_20170711232415.html

[sjczheng]

Hi, @dvantwisk

Thank you so much for your comments. I have learned a lot from it. I've made the following improvements:

DESCRIPTION L8: Using 'Imports:' instead of 'Depends'

NAMESPACE Now using importFrom()

R

R/DummyBeta.m.R & R/centDHSblood.m.R More description added

R/epidish.R

L94: Putting argument validation upfront instead of at end of function. Using match.arg().

L101: Putting argument validation upfront instead of at end of function. Using match.arg(). . Making 'constraints' in function definition equal to c('inequality', 'equality').

All: Using seq_len() instead of : in the for-loop.

L168-170: Vectorized with: s <- seq_len(ncol(avdata.m)) rmse.m[s,nui] <- sqrt(colMeans((data2.m[,s] - reconst.m[,s])^2))

L171: Using message() instead of print.

L187-192: Replacig with: D <- apply(ref.m, 2, function(x) colSums(x * ref.m))

L196-201: I cannot simplify the code as in your comments for this one. I have 0, 1, -1 in the matrix. Your comment here seems to give different result.

L194-247: If and else chunks are more concise now.

I have used the formatR package for cleaning up indentation in this file.

test

Using testthat package to test the n. of columns consistency

[dvantwisk]

The changes look great so far! We only have one change left to recommend:

R/epidish.R L191-196: vectorize with:

A.m <- matrix(0, nrow=nCT, ncol=nCT)
diag(A.m) <- rep(1, nCT)
A.m <- cbind(rep(coe.v[1], nCT), A.nCT)

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

ad61198 vectorize epidish L191

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/EpiDISH_buildreport_20170717131922.html

[sjczheng]

Hi, @dvantwisk

Thanks again for the comment. I have replaced those lines with vectorized codes.

Best regards, Charles

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

45d66a6 update epidish man file

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/EpiDISH_buildreport_20170717165430.html

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor svn repository and nightly builds. Additional information will be sent to the maintainer email address in the next several days.

Thank you for contributing to Bioconductor!