similar to: R CMD check --as-cran and (a)spell checking

Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error: > library(samr)Loading required package: imputeLoading required package: matrixStats Attaching package: ?matrixStats? The following objects are masked from ?package:Biobase?: ? ? anyMissing, rowMedians Warning messages:1: package ?samr? was

Sorry forgot to use plain text format, hope this time it works: Hi, I am trying to using SAMseq() to analyze my RNA-seq experiment (20000 genes x 550 samples) with survival endpoint. It quickly give the following error: > library(samr) Loading required package: impute Loading required package: matrixStats Attaching package: ?matrixStats? The following objects are masked from

I have a question about shallow copies in R. Since R 3.1.0, subsetting a dataframe with respect to its columns no longer result in deep copies. This is an amazing change in my opinion. Now, subsetting a data.frame by rows (or subsetting a matrix by columns or rows) still does deep copies. In particular, it is my understanding that running a command on a very large subset of rows (say

Hi, May be this helps: ?set.seed(24) ?mydata4<- as.data.frame(matrix(sample(1:100,10*38,replace=TRUE),ncol=38)) ?dim(mydata4) #[1] 10 38 ?library(matrixStats) res<-do.call(cbind,lapply(1:400, function(i) {permutation<-sample(mydata4); (rowMeans(permutation[,1:27])-rowMeans(permutation[,28:38]))/(rowSds(permutation[,1:27])+rowSds(permutation[,28:38]))} )) ?dim(res) #[1]? 10 400 A.K.

Hi, I've got a version of rowMedians(x, na.rm=FALSE) for matrices that handles missing values implemented in C. It has been optimized for memory and speed. To avoid coercing integers to doubles, and hence allocate an additional 200% memory, there is one C function for integers and one for doubles. The rowMedians() implementation is currently sitting in my non-CRAN package R.native

If I type a character using \U syntax that has more than 4 digits, I get the wrong character. For example, "\U1d4d0" should print a mathematical bold script capital A. See http://www.fileformat.info/info/unicode/char/1d4d0/index.htm On my machine, it prints the Hangul character corresponding to "\Ud4d0" http://www.fileformat.info/info/unicode/char/d4d0/index.htm It seems

Just following up on this old thread since matrixStats 0.53.0 is now out, which supports this use case: > x <- rep(TRUE, times = 2^31) > y <- sum(x) > y [1] NA Warning message: In sum(x) : integer overflow - use sum(as.numeric(.)) > y <- matrixStats::sum2(x, mode = "double") > y [1] 2147483648 > str(y) num 2.15e+09 No coercion is taking place, so the

It looks like OP uses a data.frame, so in order to use matrixStats (I'm the author) one would have to pay the price to coerce to a matrix before using matrixStats::rowMaxs(). However, if it is that the original data could equally well live in a matrix, then matrixStats should be computational efficient for this task. (I've seen cases where an original matrix was turned into a data.frame

Hi, I have a 250,000 by 300 matrix. I am trying to calculate the median of those columns (by row) with column names that are identical. I would like this to be efficient since apply(x,1,median) where x is created by choosing only those columns with same column name and looping on this is taking a really long time. Is there an efficient way to do this? Thanks! [[alternative HTML version

Hi Martin, Henrik, Thanks for the follow up. @Martin: I vote for 2) without *any* hesitation :-) (and uniformity could be restored at some point in the future by having prod(), rowSums(), colSums(), and others align with the behavior of length() and sum()) Cheers, H. On 01/27/2018 03:06 AM, Martin Maechler wrote: >>>>>> Henrik Bengtsson <henrik.bengtsson at gmail.com>

On Tue, Feb 20, 2018 at 11:58 AM, Bert Gunter <bgunter.4567 at gmail.com> wrote: > Ista, et. al: efficiency? > (Note: I needed to correct my previous post: do.call() is required for > pmax() over the data frame) > > > x <- data.frame(matrix(runif(12e6), ncol=12)) > > > system.time(r1 <- do.call(pmax,x)) > user system elapsed > 0.049 0.000

Aaaah ... and argh - I should have better not to post R question at midnight, especially when I know it forks the process and it's not using threads. Brain meltdown. (So, we'll proceed trying to use pthreads in matrixStats also for Windows). Sorry for the noise and thanks Kasper. Henrik On Aug 15, 2015 02:52, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com> wrote:

Great spot, thanks Mark. This really ought to appear somewhere in the ?Quotes help page. Having a warning under Windows might be nicer behaviour than silently returning the wrong value too. On 4 December 2014 at 22:24, Mark van der Loo <mark.vanderloo at gmail.com> wrote: > Richie, > > The R language definition [1] says (10.3.1): > > \Unnnnnnnn \U{nnnnnnnn} > (where

Hola Jorge, muchas gracias por tu pronta respuesta, no me di cuenta que el formateo podría causar problemas, envío de nuevo el código sin formatos. La idea básica es para un set de números de columnas (desordenados) y un set de numeros de fila el loop lo que hace es ir a la fila y columna correspondiente de data, tomar el valor y luego hacer la media sobre esos.

On Windows there are a few 'pthreads' implementation, e.g. pthreads-w32 and winpthreads [https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Using-pthreads]. We're thinking of giving them a try for the matrixStats package, and basic tests indicates it works, but since Windows pthreads are not used by core R (or?) I've got a little bit worried that we will face overwhelming

Hi All, I am trying to make R package using R 2.6.2 And I am getting following error. When I give R CMD check t1\ ---------- Making package t1 ------------ adding build stamp to DESCRIPTION making DLL ... making CGHseg_rewrite.d from CGHseg_rewrite.c making rowMedians.d from rowMedians.c making runavg.d from runavg.c gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c

Hi everyone, I have just started using R, and I have a simple question. How can I get the Standard deviation for rows. basically I am looking for something like "rowMeans()" but for Standard deviation (I tried "rowSds()" didn't exist) Thanks, -- View this message in context: http://www.nabble.com/Standard-deviation-for-rows-tp19998106p19998106.html Sent from the R

Muchas gracias a ambos Carlos y Jorge por las respuestas. Pido disculpas en la demora de respuesta, pero estuvo complicada la semana. La pregunta era un ejercicio de ejemplo para poder entender mejor los usos, creo que me armaré una guía en markdown con ejemplos varios para ir consultando cuando me salgan dudas de como usarlos. En realidad no importaba tanto si mejorara demasiado los tiempos

Hi. I noticed that Brian Ripley found and corrected a bug in MinGW's ld.exe, see http://www.murdoch-sutherland.com/Rtools/. Thanks for this. I wonder if this is the same bug that cause my problems. I have tiny toy package with C code that installs perfectly on R Version 2.2.1 beta (2005-12-18 r36792) [this version was mislabelled "beta" the first few hours on CRAN when the stable

I'm trying to help someone to troubleshoot possible OSX Yosemite issues, but I've only got access to OSX (< 10.9) so I cannot check myself. When building/installing binary R packages, there are different binaries depending on OSX version. For instance, CRAN provides different binaries for 'OS X Snow Leopard' and 'OS X Mavericks', e.g.