search for: rowmedians

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...

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 CGHseg_rewrite.c -o CGHseg_rewrite.o gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wall -c rowMedians.c -o rowMedians.o gcc-sjlj -std=gnu99 -Ic:/R/R-2.6.2/include -O3 -Wal...

Hi is anybody aware of a function to calculate a the median for specified columns in a dataframe or matrix - so analogous to rowMeans? Thanks Max --

...305) as well as R Version 2.3.0 Under development (unstable) (2006-02-02 r37243), I get the following error: C:\Documents and Settings\hb\braju.com.R\R.native\build>Rcmd install R.native ---------- Making package R.native ------------ adding build stamp to DESCRIPTION making DLL ... making rowMedians.d from rowMedians.c gcc -IC:/PROGRA~1/R/R-2.2.1pat/include -Wall -O2 -c rowMedians.c -o rowMedia ns.o ar cr R.native.a rowMedians.o ranlib R.native.a windres --include-dir C:/PROGRA~1/R/R-2.2.1pat/include -i R.native_res.rc -o R. native_res.o gcc --shared -s -o R.native.dll R.native.def R.na...

...clude -fpic -g -O2 -c matchpt.c -o matchpt.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include -I/usr/local/include -fpic -g -O2 -c Rinit.c -o Rinit.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include -I/usr/local/include -fpic -g -O2 -c rowMedians.c -o rowMedians.o gcc -std=gnu99 -I/usr/local/lib64/R/include -I/usr/local/lib64/R/include -I/usr/local/include -fpic -g -O2 -c sublist_extract.c -o sublist_extract.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o Biobase.so anyMissing.o envir.o matchpt.o Rinit.o rowMedians.o sublist_extract.o...

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

...set: ISO8859-1 * checking for file 'matrixStats/DESCRIPTION' ... OK * this is package 'matrixStats' version '0.12.0' * checking CRAN incoming feasibility ... NOTE Maintainer: 'Henrik Bengtsson <henrikb at braju.com>' Possibly mis-spelled words in DESCRIPTION: rowMedians (18:74) rowRanks (18:92) rowSds (18:111) * checking package namespace information ... OK ... Thanks Henrik

Dear R gurus, I have been struggling with this for a while and thought you might be able to give me some guidance. I have a data frame, on which I apply a row function. The result looks to me like a vector that retains the old row names. I then sort the vector and subsequently need to be able to identify the rank of certain values by searching for their row names. See this mock example: >

...A-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 built under R version 3.3.3?2: package ?matrixStats? was built under R version 3.3.3 > samfit<-SAMseq(data, PFI.time,censoring.status=PFI.status, resp.type="Survival") Estimating sequencing depths...Error in quantile.default(prop, c(0.25, 0.75)...

Hello All, I need your help. I am analysing affymetrix data and have to select the probe-set that has median expression among all the probe-sets for same gene. This way I want to remove the redundancy by keeping the analysis to single gene entry level. I am fully aware that it is not a nice thing to do but I just have to do it. To do so, I came across 'findLargest' function of

...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 ?package:Biobase?: ? ? anyMissing, rowMedians Warning messages: 1: package ?samr? was built under R version 3.3.3? 2: package ?matrixStats? was built under R version 3.3.3 > samfit<-SAMseq(data, PFI.time,censoring.status=PFI.status, resp.type="Survival") Estimating sequencing depths... Error in quantile.default(prop, c(0.25,...

The "micEcon" package has been split into three packages: miscTools, micEconAids, and micEcon. a) miscTools (version 0.6-0) includes miscellaneous small tools and utilities that are not related to (micro)economics, e.g. colMedians(), rowMedians(), insertCol(), insertRow(), vecli(), symMatrix(), triang(), semidefiniteness(), compPlot(), and rSquared(). The miscTools package should depend on (almost) no other packages so that it can be used in other packages without increasing the total (recursive!) dependencies of these packages too much....

The "micEcon" package has been split into three packages: miscTools, micEconAids, and micEcon. a) miscTools (version 0.6-0) includes miscellaneous small tools and utilities that are not related to (micro)economics, e.g. colMedians(), rowMedians(), insertCol(), insertRow(), vecli(), symMatrix(), triang(), semidefiniteness(), compPlot(), and rSquared(). The miscTools package should depend on (almost) no other packages so that it can be used in other packages without increasing the total (recursive!) dependencies of these packages too much....

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