lshep
commented
8 years ago Thank you for your submission. Please address the following issues:
General: remove the png in the top level directory
generally we like packages to be under 4Mb after running R CMD build. Is there any way to reduce your package size, perhaps a smaller dataset?
Vignette:
We suggest using the BiocStyle::html_document as the output format and therefore add BiocStyle to suggest in the DESCRIPTION file.
Please change or also include installation instruction through Bioconductor
source("http://www.bioconductor.org/biocLite.R")
biocLite("MONSTER")When you describe setting up the design vector, you describe it as a 10/5/10 inclusion/exclusion but in the code it looks like 20/10/20 ?
It seems like you make wrappers for ggplot (tranisitionPCAPlot), igraph (transitionNetworkPlot), dTFIPlot (plot) , why wouldn't you have such a wrapper for the heatmap?
It seems like the input arguments for monster can be an exprSet/expressionSet for the motif/exprData (or at least they should be). It would be nice to see examples in vignette and man pages and make this more clear. We really try to foster the interconnectivity and compatibility with standard Bioconductor objects.
MAN PAGES:
general:
Change all keywords to meaningful keywords or exclude not \keyword{keyword}
If you have internal functions they should be marked as \keywork{internal}, possibly functions you haven't exported
bereFull.Rd/ldaBERE.Rd: add example
checkDataType.Rd: either mark as internal or export and add example
monster-package.Rd: remove references if not populated add \seealso section linking to the man page for monster function remove examples section or include an example don't just populate with comments
monster.Rd: Can expr be an ExpressionSet (it should) - make this more clear Can motif be matrix, exprSet (it should), data.frame that you made reference to in other help pages? - make this more clear. outputDir should be more clear that its a character vector for the path of file, not logical T/F Add more details to the MONSTER algorithm, not everyone will look at vignette or where to find it, should be a brief summary here Add a \seealso to link to a man page for your monster object
ADD A PAGE FOR YOUR CLASS/OBJECT! - currently have no idea what the 'monster obj' is. There should be a page documenting its structure and what is stored.
monsterNI.Rd: 'alphaw' - what documentation?
plot.monster.Rd: '...' what other plotting methods? what is the underlying plotting function
ssodm.Rd: Shouldn't this also be able to take in your monsterObj? The code probably should be altered as such.
transformation.matrix.Rd: What are the acceptable values for 'method'
R/CODE: general: Remove any "::", they shouldn't be needed if specified in NAMESPACE/DESCRIPTION Use seq_len/seq_along rather than 1:n/1:length(x) where appropriate
Class: Can your output extend any existing Bioconductor structures? I would offer suggestions but with no man page describing the existing structure and what it consists of its challenging.
analysis_functions.R: Be consistent with naming - functions that use monsterObj as input sometimes are labelled function(x, ...) while others are function(monsterObj, ... )
plottm This is not used anywhere, not exported, and not documented. Can it be removed?
hcl.heatmap.plot Take out commented code/test code
ssodm This should take in your monsterObj instead of or in addition to a matrix?
transformation.matrix Have a check for valid 'method' Take out commented out code
globalVariableHack.R: globalVariables should be defined where they are used, in general we don't like 'hacks'. This file shouldn't exist
regpredict.R: monsterNI: Check valid 'method' since stated in the help page only certain are valid. If 'cd', 'lda' or 'wcd' are used, they all are the same method?
monster: Can motif really be NULL? it doesn't appear so? have a check? Make sure input can also be standard Bioconductor objects like exprSet/expressionSet.
Thank you for your submission. Please address the above issues with updates or justification. Lori
bioc-issue-bot
dschlauch
Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor
Confirm the following by editing each check box to '[x]'
I am familiar with the essential aspects of Bioconductor software management, including:
For help with submitting your package, please subscribe and post questions to the bioc-devel mailing list.