Thanks so much for your comments and help! Best, Dongmei
From: Gabe Becker [mailto:becker.g...@gene.com] Sent: Friday, February 20, 2015 9:33 AM To: Li, Dongmei Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] A quick questions on writing R functions Dongmei, This isn't really the right list for this type of question. That said, I can give you a few pointers. The actual section of the manual you quoted is about documenting your function, not the code of the function itself. That said, "eval" is not a good name for your function. It doesn't tell the caller what the function is going to do, and it will mask the eval function in base (this is unlikely to actually cause any problems, but it's bad practice). This function could also be vectorized if you turn it into a an elementwise comparsion of two matrices followed by a call to colSums. Even if not, I suspect that reptition is simply the length of the vectors you pass in? If so, just call mean on the logical vectors, no need to add them and divide as a separate step (though admittedly that isn't really going to save you much). ~G On Fri, Feb 20, 2015 at 6:10 AM, Li, Dongmei <dongmei...@urmc.rochester.edu<mailto:dongmei...@urmc.rochester.edu>> wrote: Hi, I'm developing an R package and got the following suggestions for revising the functions: "When a function returns a named list, a good practise is to start the \value section with the following: A named list with the following components: and then to itemize the components" This is an example of my current function: eval<- function (ord_vec_t, ord_vec_pvalue, eval_matrix_t, eval_matrix_pvalue, repetition) { rowsdim <- length(ord_vec_t) p_pvalue <- rep(NA, rowsdim) p_tstat <- rep(NA, rowsdim) for (g in 1:rowsdim) { p_pvalue[g] <- sum(eval_matrix_pvalue[g, ] <= ord_vec_pvalue[g])/repetition p_tstat[g] <- sum(abs(eval_matrix_t[g, ]) >= abs(ord_vec_t[g]))/repetition } mylist <- list(p_pvalue = p_pvalue, p_tstat = p_tstat) return(mylist) } Anyone could offer some suggestions on revising the function based on the comments? Thanks so much for all your help! Best, Dongmei _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel<https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=AwMFaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=azjhQW59umxfk67jsIXeg7AS2ugqKLkykGYJFRwaLto&m=qqsvuTQftkkIrTwQWWynG_Y_UWBGtmC2pUjlk0C4Tss&s=I1Rjmnpu9a8_u14tWmTe-mwgwqTItRQOpIy_9uork8Y&e=> -- Gabriel Becker, Ph.D Computational Biologist Genentech Research [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
