search for: termiso

Hi all, I've got a matrix of fractional data that is all positive and greater than zero that I would like to "loosely" classify, for lack of a better word. It looks something like this : 1.07 1.11 1.27 1.59 0.97 0.76 2.23 0.98 0.71 0.88 1.19 1.02 What I'm looking for is a way to round these numbers to the nearest 0.25, i.e. the above matrix would be

Hi all, I've got a package i've written that i am trying to check, build, and install. This is my 1st time doing this, so apologies in advance... ;) The package that I've written requires input from the user. It needs to know sample sizes and then runs some calcs, (sample sizes are just integers), and it gets this info from the user as num_reps <- readline("How many reps

Hello, I'm hoping that there is an easier way to rename columns in a data frame other than by using the names() assignment, which requires you to type in all the column names at once for a data.frame, in the case that I simply want to rename a single column in a data frame. Also, is there an easy way to move columns in a data frame around relative to the other columns? Thanks in

...want to do this in a plain R file, (e.g. package/tests/somename.R), you can use if(interactive) { num_reps <- readline(""How many reps do you have... ") num_reps <- as.integer(num_reps) } else num_reps <- 10 instead. -G > -----Original Message----- > From: Ken Termiso [mailto:jerk_alert at hotmail.com] > Sent: Monday, October 03, 2005 11:42 AM > To: Warnes, Gregory R; ripley at stats.ox.ac.uk > Cc: r-help at stat.math.ethz.ch > Subject: RE: [R] Problem building/checking library that requires input > from user > > > Thanks, Dr Warnes &am...

Hi all, As far as I can tell, the only canned way to do an intersect between two vectors of ints is the intersect(vec1, vec2) function -- is there another function I'm missing for intersecting more than two vectors?? TIA, Ken

Hi all, What I'd like to do is to is to be able to extract a string corresponding to only the file name from a string containing the complete path, i.e. from the following path string: "/Users/ken/Desktop/test/runs/file1" I would like to end up with: "file1" This would be most ideally done in a platform-independent way. Thanks in advance, -Ken

Hi all, Sorry if this is a dumb question, but I am on 10.4 with R2.2, and when loading a big text file (~500MB) with scan(file, what=character) I am throwing malloc errors that say I am out of memory...I have 5GB on this machine, and Activity Monitor tells me R is only up to ~1.84GB both times this has happened (running from terminal)... I am wondering why this is happening when I still have

Hi all, I've got a script that generates a few moderate-size data frames, and then puts them together into one big data frame at the end in order to write that data frame to disk, so that it may be re-opened later on... I'm trying to trim down memory requirements in this script, so I was wondering if there was any way to append to a data frame already saved on disk (just like

Hi all, I've got a data frame that has an identical column to a chr vector. I would like to use the chr vector to order the rows of the data frame to be identical to the order in the chr vector (the contents of the chr vector are completely identical to one col of the data frame), but this is proving trickier than it sounds.. Any help would be much obliged, -Ken

Hi all, I have a vector that contains the row numbers of data taken from several filtering operations performed on a large data frame (20,000rows x 500cols). In order to output this subset of data, I've been looping through the vector containing the row numbers (keepRows). output <- data.frame(row.names = rownames(bigMatrix)) for(i in keepRows) { output <- rbind(output,

Hi all, I've got a script that I run on several computers, some with much less ram than others, and I would like to try and keep the memory usage as low as possible. The script creates variables to store intermediate results of calculations, and then at the end writes a text file with the results of the calculations. Is a quick and dirty way to accomplish this to use rm() to delete

Hi all, I was hoping that someone could verify this for me- when I run princomp() on a matrix, it is my understanding that the scores slot of the output is a measure of how well each row correlates (for lack of a better word) with each principal component. i.e. say I have a 300x6 log2 scaled matrix, and I run princomp(). I would get back a $scores slot that is also 300x6, where each value

Hi all, When using heatmap() with a pdf driver, and specifying parameters for mai in heatmap, I get a printout of the mai parameters at the top of the pdf...see attachment. This is on win2k pro with R2.2.1 Thanks, Ken

Having a very strange and frustrating problem with v2.0.1 under Mac OSX 10.3. I have several closely related workspaces in the same directory that I need to keep separate from one another (there are a few objects common to all workspaces, and then there are other objects that store the results of different analyses on the common objects, which is why I need separate workspaces). When I

Hi all, I have a bunch of int vectors. Each vector holds a bunch of ints that correspond to row numbers of an existing matrix. I use the int vectors to pull out rows of data from a matrix, i.e. data <- my_matrix[int_vector,] I would like to store these int vectors in some sort of data structure that will preserve them as-is and allow iteration. I guess what I'm looking for would be

Hello all, I'm using the following scan() parameters on a tab-separated text file that was generated by R. temp_file <- scan(file = outfile, sep="\t", what = character(), skip = 1, nlines = 1) The problem is that within some cells, there are cases where there are three frontslashes ( /// ). However, the file itself is tab-separated, and the exact problem is that even if I

Hi all, I searched through the archives, but couldn't find a fix... Basically, I've got a bunch of numeric vectors and one character vector that I want to bind into a data frame. When I include the character vector as a column in the data frame, all the numeric columns get factored in the data frame, which makes it tough to call those columns for calculations later on. I've tried

Hi, I've got a library I'm trying to build, and am having an error on R CMD check... The source is fine, and the script runs OK, but during the script test execution it downloads a library from an online repository, which goes fine and it says that installation was successful... However, after it installs the library OK, it then cannot find it (despite it being installed properly in

Hi all, I originally posted this to the bioconductor group, but maybe it's better suited to the r-help... I'm using som() to partition samples of gene expression data into clusters. The point is to classify control vs. experimental cases (sample clustering). The original matrix was 22283 x 8. The 8 samples have 4 controls and 4 experimentals. I transposed the matrix so that its dim

I realize that others have struggled with this issue...i.e. http://tolstoy.newcastle.edu.au/~rking/R/help/05/01/9826.html i am on os.x 10.4 w/ R2.2, and am (perhaps foolishly) also on this quest... i would like to be able to install downloaded source (tar.gz'd) files from within an R session, and have it work in a X-platform way..i am often not connected to the internet and have libraries