similar to: efficiently replacing values in a matrix

Hi, Suppose I have the following tabular data: 1729_at | TRADD | TNFRSF1A-associated via death domain | protein-coding 1773_at | FNTB | farnesyltransferase, CAAX box, beta | protein-coding 177_at | PLD1 | phospholipase D1, phosphatidylcholine-specific | protein-coding What is the right separator used for read.table function? I tried this: dat <-

This question attacked me as I was thinking about matrix value updates. I probably will never need to do this, but wanted to ask if there are efficient methods to perform the for-loop in the following sequence. %xymat<-matrix(rep(0,100) nr=10,nc=10) # empty matrix %x<-1:10 %y<-sample.int(10,10,rep=T) %for (j in 1:10) xymat[x[j],y[j]] <- some_function(x[j],y[j]) #to create either

Hello, I am working multiple simulated data sets with missing values, I would like to store these data sets in either tab delimited format for .csv format with missing values marked as NaN's instead of NA's. I read the import/export document which mentions that write.table command converts NaN's to NA. Is there any other way I can store the NaN's. I tried the write syntax

Hi, I have a problem with a package I have developed in that functions do not get loaded due to older versions of the functions being in the .GlobalEnv? fetched from .Rdata files stored from previous saved workspaces. I need to be able to fix this somehow when I load the package. I do not want to mess up the search order to fix the problem. How I got myself into this mess is that I started

Hi, I'm a biologist, so please forgive me if my question sounds absurd! I have 3 parameters x1, x2, x3 and a response variable y.The sample size is 75. I tried to do the following: mylm<-lm(y~ x1 + x2 + x3, data="mydata") but i can only get stats from anova for the first 2 variables. The third comes up as NA. The degrees of freedom for the third variable are 0. Is there

Hi all, Probably a rudimentary question. I have a flat file that looks like this (the real one has ~10e6 elements): 10110100101001011101011 and I want to pull that into R as a vector, but with each digit being it's own element. There are no separators between the digits. How can I accomplish this? Thanks in advance! Matt -- Matthew C Keller Asst. Professor of Psychology University of

Hi all, Is there a way to skip non-sequential lines using the "skip" argument in the scan function? E.g., I have a matrix with 100 rows and 1e7 columns. I open a connection and want to read only lines 5, 7, 9, etc [i.e., seq(5,99,2)] It might seem that the syntax to do this would be something like this (if only the "skip" allowed vectors in the same way colClasses does in

Hi all, Perhaps this is more of a unix question, but I'll give it a try here. I am running 9 different R processes at the same time (called from a shell script using R CMD BATCH). When I use the top program to monitor how they are doing, it is impossible to tell which R process is related to which R script. Is there a way to rename a specific instantiation of an R process in top with

I have recently been bitten by an aspect of the behaviour of the read.csv() function. Some lines in a (fairly large) *.csv file that I read in had too many entries. I would have hoped that this would cause read.csv() to throw an error, or at least issue a warning, but it read the file without complaint, putting the extra entries into an additional line. This behaviour is illustrated by the toy

hi all, I'm full of questions today :). Thanks in advance for your help! Here's the problem: x <- c('18x.6','12x.9','302x.3') I want to get a vector that is c('18x','12x','302x') This is easily done using this code: unlist(lapply(strsplit(x,".",fixed=TRUE),function(x) x[1])) So far so good. The problem is that x is a vector

Hello all, I hate to add to the daily queries regarding R's handling of large datsets ;), but... I read in an online powerpoint about the ff package something about the "length of an ff object" needing to be smaller than .Machine$integer.max. Does anyone know if this means that the # of elements in an ff object must be < .Machine$integer.max [i.e., that ff provides no help with

Hi all, My graduate student is logging onto my macpro and running R through ESS aquamacs (with Mx ssh and then Mx ess-remote). Everything is working fine until we get to graphing. We are trying to give him the ability to look at graphics interactively. The ESS manual is not too helpful: "If you run X11 (See Section 13.3.2 [X11], page 68, X-windows) on both the local and remote machines

Hi all, I have a vector, most of which is missing. The data is always increasing, but may do so in jumps. I would like to interpolate the NAs with 'best guesses', using something like filter(), which doesn't work due to the NAs. Here is an example: > x <- c(2,3,NA,NA,NA,3.2,3.5,NA,NA,6,NA) > x [1] 2.0 3.0 NA NA NA 3.2 3.5 NA NA 6.0 NA I would like a function that

Hi all, I've had one of my most miserable R weeks in memory. I'm trying to deal with huge datasets (>1GB each) but am running up against those pesky memory limits. The libraries filehash and g.data are not very suitable for what I need. I haven't gotten into the sql thing yet. Most recently I've been trying to install the new package ff (not yet on the CRAN repository). I

There appears to be a bug in help() when there are multiple packages attached containing functions with the same name, and offline=TRUE. Example: library(mgcv) library(gam) If one simply does: help(gam) # No ``offline=TRUE'' then the following message appears: Help on topic 'gam' was found in the following packages: Package Library mgcv

Hi all, I used to use fwrite() function in data.table but I cannot get it to work now. The function is not in the data.table package, even though a help page exists for it. My session info is below. Any ideas on how to get fwrite() to work would be much appreciated. Thanks! > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Red Hat

Hi Matt Your method is the easiest way for me to install the 64-bit R. I followed the directions on your web site and then did the following: R --arch=x86_64 source("http://bioconductor.org/biocLite.R") biocLite(type = "source",lib = "/Library/Frameworks/R.framework/Versions/2.8/Resources/RLib64") I got many errors and warnings which I copied to the attached file.

Hello all, I have some genetic datasets (gzipped) that contain 6 columns and upwards of 10s of billions of rows. The largest dataset is about 16 GB on file, gzipped (!). I need to sort them according to columns 1, 2, and 3. The setkey() function in the data.table package does this quickly, but of course we're limited by R not being able to index vectors with > 2^31 elements, and bringing

Hi all, SETUP: I have pairwise data on 22 chromosomes. Data matrix X for a given chromosome looks like this: 1 13 58 1.12 6 142 56 1.11 18 307 64 3.13 22 320 58 0.72 Where column 1 is person ID 1, column 2 is person ID 2, column 3 can be ignored, and column 4 is how much chromosomal sharing those two individuals have in some small portion of the chromosome. There are 9000 individual people, and

Hi all, I'm on a Linux server with 48Gb RAM. I did the following: x <- big.matrix(nrow=20000,ncol=500000,type='short',init=0,dimnames=list(1:20000,1:500000)) #Gets around the 2^31 issue - yeah! in Unix, when I hit the "top" command, I see R is taking up about 18Gb RAM, even though the object x is 0 bytes in R. That's fine: that's how bigmemory is supposed to