Jeff, Thanks for the help. I should have thought of passing na.rm to sum. This worked nicely.
Scott Scott A. Ochsner, PhD One Baylor Plaza BCM130, Houston, TX 77030 Voice: (713) 798-6227 Fax: (713) 790-1275 -----Original Message----- From: jsp...@gmail.com [mailto:jsp...@gmail.com] On Behalf Of Jeffrey Spies Sent: Friday, October 01, 2010 10:13 AM To: Ochsner, Scott A Cc: r-help@r-project.org Subject: Re: [R] Need to incorporate the use of na.rm into custom function You can use na.omit on x after it is passed into your apply function if na.rm == T, or simply pass your na.rm to functions that use it, such as sum. Hope that helps, Jeff. On Fri, Oct 1, 2010 at 11:07 AM, Ochsner, Scott A <sochs...@bcm.edu> wrote: > Hi, > > Take a matrix with missing values: > >> X = matrix(rnorm(10), ncol = 5) >> X[2,4]=NA >> X > [,1] [,2] [,3] [,4] [,5] [1,] > -0.1566427 -0.7382232 -1.0564624 -0.8412139 0.9370319 [2,] -1.0289865 > -0.8452054 -0.1349459 NA -0.1749113 > > I want to apply a custom function over the rows such that the NAs are ignored > in a similar fashion as to how the following works. > >> means<-apply(X,1,mean,na.rm=TRUE) > > Custom function: > > liptak<-function (x,df) > 2*(pnorm(abs(sum(x*df)/sqrt(sum(df^2))),lower.tail=FALSE)) > > I want to be able to do the following: > >>rslt<-apply(X,1,liptak,na.rm=TRUE) > > Can someone point me in the right direction on how to incorporate the use of > na.rm into my function? > > > Scott > >> sessionInfo() > R version 2.11.0 (2010-04-22) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > Scott A. Ochsner, PhD > NURSA Bioinformatics > Baylor College of Medicine > One Baylor Plaza > Mail Stop: BCM-130 > Houston, TX 77030 > Voice: (713) 798-6227 > Fax: (713) 790-1275 > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
