Improvements to API: formatting, namespace, dependencies, sanity checks, output #1
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+ convert tabs to spaces
+ keep line length to <= 90 characters
+ spaces after commas and between '='
+ only function names should have '.' in label
+ reduce whitespace between '(' and between lines
+ no longer depend on limma and igraph; rather they are now imported using '::' operator + added explicit reference to pcaPP package, which is required for any use of 'cor.fk' + added explicit reference to KEGGgraph package, which is required to handle the data files + added all packages to 'imports' section in DESCRIPTION file; thus, these packages are installed when genesurrounder is installed + added importFrom statements so that the imported methods are in NAMESPACE
+ exporting these methods now make them visible to user + exported methods are now in NAMESPACE + calcCorMatrix now has default options for 'corMethod' and 'useMethod'; these would not be known by the casual user + switch order of arguments to calcAllPairsDistances; this makes it easier for the user which arguments are required.
…d 'all' option for 'genes_assayedETnetwork' argument
+ can now take an arbitrary plot title + now plots the line indicating maximum number of genes tested, taken directly from the results + added documentation + added graphics to dependencies + updated namespace
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Hi @sahildshah1,
Here are some commits to help push the codebase closer to being a package that could be submitted to CRAN or bioconductor.
Summary of the changes:
DESCRIPTIONfile with package dependenciescalcAllPairsDistances,calcCorMatrix,calcGeneTStats,geneNIDGdevtools::documentand theroxygen2syntax for documenting)NAMESPACEto import necessary methods for the functions that need them (the@importFromsyntax withinroxygen2comments)geneNIDGoutput, combining the DE-decay p-value and the Correlation p-valueRemaining to-dos: