Conform to Bioconductor guidelines

[j-lawson]

https://www.bioconductor.org/developers/package-guidelines/

Key points:

• 1. The majority of exported functions (all if possible) should have examples in documentation (@examples). Plots should be assigned to an object, not displayed (myPlot = plottingFunction(x))

• 2. Follow "R Code and Best Practices" section in link above. These will be flagged by Bioconductor when checking the package:

  • Use vapply() instead of sapply() and use the various apply functions instead of for loops.
  • Use seq_len() or seq_along() instead of 1:...
  • Use TRUE/FALSE instead of T/F
  • Avoid class()== and class()!= instead use is()
  • Use system2() instead of system
  • Do not use set.seed in any internal R code.
  • No browser() calls should be in code
  • Avoid the use of <<-.
  • Avoid use of direct slot access with @ or slot(). Accessor methods should be created and utilized
  • Line length <= 80 characters, including for documentation lines

• 3. Unit tests for main package functions highly recommended.

• 4. Validity checks for function input

• 5. Package dependencies need to be noted in "Depends/Imports/Suggests/Enhances" field. See link above for guidance on which.

• 6. Package data used for examples and vignettes should be minimal amount needed. Files should be compressed to decrease file size like so: save("esr1_chr1", file = "esr1_chr1.RData", compress = "xz")

• 7. Package data should be documented in data.R file according to BIOC standards. (See https://github.com/databio/COCOA/blob/master/R/data.R for example)

[kkupkova]

I fixed few of the sapply functions - those are now vapply. But I wasn't able to fix all of them.

[joseverdezoto]

@kkupkova what plot functions/scripts did you change?

[kkupkova]

Just the recursions in plotting functions