VULCAN: VirtUaL ChIP-Seq data Analysis using Networks

federicogiorgi commented 7 years ago

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federicogiorgi commented 7 years ago

@nturaga I implemented all the changes you suggested.

There is nothing I can do about the single warning, which seems to be on the server side: "Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11)."

Also, 9 lines (0%) are not indented with multiples of 4 spaces, but those are man pages automatically generated by roxygen2.

nturaga commented 7 years ago

Hi @federicogiorgi

I'll review your package again soon. But you need to fix a couple of things before that.

Your formatting seems to have disappeared entirely on your R code.
vobj in vulcan, is a list containing samples, peak counts, and other data.frames, why not describe the contents of the list in the man pages.

Please update the man pages, to be more informative, wherever else needed.

federicogiorgi commented 7 years ago

Thanks @nturaga. OK give me some time to manually fix every single line. The tidy_source function from formatR cannot at the same time force line length below 80 columns and transform indentation in multiples of 4 white spaces, for some reason. Ha, I've spent 90% of this package time on formatting indentation, no jokes :-)

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federicogiorgi commented 7 years ago

@nturaga I have updated the man pages with extra info and reformatted the indentation of the source code :-) Again, I get this single server-side (I think) warning: "Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11)."

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federicogiorgi commented 7 years ago

@nturaga and all: I implemented all the suggested fixes, the package is ready for your inspection :-)

federicogiorgi commented 7 years ago

@lshep @mtmorgan @nturaga All the suggested fixes have been fixed a few weeks ago, the package is ready for your inspection :-)

nturaga commented 7 years ago

I'll have your second-review done by mid next week.

federicogiorgi commented 7 years ago

Any news on the second review? :-)

nturaga commented 7 years ago

Please import to fix that NOTE.

Consider adding
  importFrom("graphics", "abline", "grid", "layout", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "ks.test", "pchisq", "pnorm", "pt", "qnorm", "qt",
             "rnorm", "setNames")
  importFrom("utils", "read.csv", "setTxtProgressBar", "txtProgressBar")

Also needed are

importFrom("GenomicRanges", "GRanges")
importFrom("S4Vectors", "Rle")

Checking to see if we understand object initialization...
    * NOTE: Consider clarifying how 33 object(s) are initialized. Maybe
      they are part of a data set loaded with data(), or perhaps part
      of an object referenced in with() or within().
    object (function)
      Rle (average_fragment_length)
      lines (average_fragment_length)
      abline (average_fragment_length)
      legend (average_fragment_length)
      pt (corr2p)
      pchisq (fisherp)
      qt (p2corr)
      qnorm (p2z)
      ks.test (pareto.fit)
      e2s (plot_gsea)
      layout (plot_gsea)
      par (plot_gsea)
      plot (plot_gsea)
      rect (plot_gsea)
      abline (plot_gsea)
      text (plot_gsea)
      grid (plot_gsea)
      lines (plot_gsea)
      legend (plot_gsea)
      qnorm (rea)
      plot (textplot2)
      points (textplot2)
      lines (textplot2)
      text (textplot2)
      colorpanel (val2col)
      GRanges (vulcan.annotate)
      read.csv (vulcan.import)
      exprs (vulcan.normalize)
      setNames (vulcan.pathways)
      rnorm (vulcan.pathways)
      txtProgressBar (vulcan.pathways)
      setTxtProgressBar (vulcan.pathways)
      pnorm (z2p)

Many place where you remove objects in the middle of the function eg: rm(rawmat) vulcan.R, l 67, l, 82.

This is not needed, if you are rewrinting the object, by creating a new matric in l71.
In vulcan.R,

 232     ### Fix data types as needed
 233     for (j in seq_len(ncol(rawcounts))) {
 234         rawcounts[, j] <- as.numeric(rawcounts[, j])
 235     }
 236     rawcounts <- as.matrix(rawcounts)
 237
 238     for (j in seq_len(ncol(rpkms))) {
 239         rpkms[, j] <- as.numeric(rpkms[, j])
 240     }
 241     rpkms <- as.matrix(rpkms)

can be replaced with,

 rawcounts = matrix(as.numeric(rawcounts), nrow(rawcounts))
 rpkms = matrix(as.numeric(rpkms), nrow(rpkms))

Did not fix, dist_calc in vulcan.R. Lot of repeating code chunks.

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federicogiorgi commented 7 years ago

@nturaga Thank you for your review! I implemented the suggested changes

Fixed imports
Removed the unnecessary rm()
Corrected the vulcan.R lines as suggested (the suggested edit lacked dimnames, so I added that as well)
Condensed repeated lines of code in dist_calc

nturaga commented 7 years ago

@federicogiorgi

Your package times out in the build report because R CMD check takes more than 10 mins on the mac builder. Please fix this issue.

Otherwise, your package looks in good shape for acceptance.

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federicogiorgi commented 7 years ago

@nturaga not sure why the R CMD Check times out on the Mac server. It didn't before, and the recent changes I've made to the package were formalities in the code. On our Mac, it takes ~3minutes. Any suggestion?

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VULCAN: VirtUaL ChIP-Seq data Analysis using Networks #379