similar to: String frequencies in rows

Dear all, I''m trying to write a function, that will take as an argument, some aligned genome sequences, and using a sliding window, do pairwise comparisons of sequence similarity. Coding the sliding window I think I can manage but what I''m trying to get to grips with is getting it so as every pairwise comparison is made, no matter how many genomes are added, from 3 to N. So if

Hi I am using the following script to average a set of data 0f 62 columns into 31 colums. The data consists of values of ln(0.01) or -4.60517 instead of NA's. These need to be averaged for each row (i.e 2 values being averaged). What I would I need to change for me to meet the conditions: 1. If each run of the sample has a value, the average is given 2. If only one run of the sample has a

Dear R users, I have a data generated as the following, dat <- data.frame(matrix(sample(24), nrow=4)) dimnames(dat) <-list(rownames=c('g1','g2','g3','g4'), colnames=c("A_CH1","A_CH2","B_CH1","B_CH2","C_CH3","C_CH3")) » dat A_CH1 A_CH2 B_CH1 B_CH2 C_CH3 C_CH3 g1 16 24 7 9 14

There was a BioConductor thread today where the poster wanted to find pairwise difference between columns of a matrix. I suggested the slow solution below, hoping that someone might suggest a faster and/or more elegant solution, but no other response. I tried unsuccessfully with the apply() family. Searching the mailing list was not very fruitful either. The closest I got to was a cryptic chunk

We were looking at conducting a pilot program with Dell to virtualize our lab environments. We are specifically looking at Dell/Citrix provisioning servers. The OS in this setup is streamed from the server on every boot. I was curious if the R Project had any licensing stipulations in this type of setup. This is in the beginning phases and we wanted to answer some questions about licensing.

Hello, Were having issues with macs writing to our gluster system. Gluster vol info at end. On a mac, if I make a file in the shell I get the following message: smoke:hunter david$ echo hello > test -bash: test: Operation not permitted And the file is made but is zero size. smoke:hunter david$ ls -l test -rw-r--r-- 1 david realise 0 Mar 3 08:44 test glusterfs/nfslog logs thus:

Carlos: Te agradezco mucho tu rápida respuesta y mucho me apena haber planteado tan mal el problema. Porque la matriz en realidad es: g1 g2 g3 g4 g5 g6 g7 g1 0 18 13 16 11 12 15 g2 18 0 25 13 22 16 10 g3 13 25 0 28 23 13 25 g4 16 13 28 0 6 7 3 g5 11 22 23 6 0 18 17 g6 12 16 13 7 18 0 8 g7 15 10 25 3 17 8 0 Entonces cada cantidad debe conservar la pertenencia al grupo

Hi We deployed centos 4.8 on HP DL380 G2, G3 and G4 servers (same number of cpus). The same software is running on all servers. Only on G2 servers we see a low cpu utilization combined with high load-average. For example, during the same time of day and same workload, on a G2 I see a l-avg of 11.31 and on a G4 I see 2.68. The server response time seems unchanged and we don't have any problem

I'm trying to sort a DATAFRAME by a column "ID" that contains alphanumeric data. Specifically,"ID" contains integers all preceeded by the character "g" as in: g1, g6, g3, g19, g100, g2, g39 I am using the following code: DATAFRAME=DATAFRAME[order(DATAFRAME1$ID),] and was hoping it would sort the dataframe by ID in the following manner g1, g2, g3, g6, g19,

Hi All, How do I add these axis labels? ############################################### p=seq(0,1,length.out=500) p=p[-c(1,length(p))] g1=log(p/(1-p)) g2=qnorm(p) g3=log(-log(1-p)) g4=-log(-log(p)) plot(p,g1, 'n',ylim=c(-5,5),las=1, bty='n', xaxt='n',yaxt='n', xlab="",ylab="" ) lines(p,g1,lty=1,col=1) lines(p,g2,lty=1,col=2)

Dear R users, I have noted a difference in the merge distances given by hclust using centroid method. For the following data: x<-c(1009.9,1012.5,1011.1,1011.8,1009.3,1010.6) and using Euclidean distance, hclust using centroid method gives the following results: > x.dist<-dist(x) > x.aah<-hclust(x.dist,method="centroid") > x.aah$merge [,1] [,2] [1,] -3 -6

Dear R helpers,   Following is a R script I am using to run the Fast Fourier Transform. The csv files has 10 columns with titles m1, m2, m3 .....m10.     When I use the following commands, I am getting the required results. The probelm is if there are 100 columns, it is not wise to define 100 commands as fk <- ONS$mk and so on. Thus, I need some guidance to write the loop for the STEP A and

Does the "legend" command work in the windows version of R? Here is the command that I'm using: legend(1,1,legend=c("G1","G2","G3","G4","G5","G6"),pch=array(1:6,dim=c (1,6))) When I use this on my existing graph in a window I get a solid black box at the lower left. If I use this with the postscript driver my output

I have a really simple question I have a data frame of 8 variables (the first column is the subjects' id): SubID G1 G2 G3 G4 W1 W2 W3 W4 1 6 5 6 2 6 2 2 4 2 6 4 7 2 6 6 2 3 3 5 5 5 5 5 5 4 5

Hello all. I have two data frames. Group Start End G1 200 700 G2 500 1000 G3 2000 3000 G4 4000 6000 G5 7000 8000 and Pos C0 C1 200 0.9 0.6 500 0.8 0.8 800 0.9 0.7 1000 0.7 0.6 2000 0.6 0.4 2500 1.2 0.8

I have a system with two 4 port T1 cards, with 5 PRI's configured. Each PRI is configured as an individual PRI and belongs to it's own group (groups 1-5) This system is handling roll-over from another system, where any error in processing the call on that system results in it being sent here. This mainly results in all calls resulting in a busy being sent for retry here. I then

On how to even search for this "feature" as I have no idea on what it can be. I've got a meridian linked to * (by EuroISDN) which is linked to a ISDN30. I can make calls from the meridian, and receive calls into the meridian. Great stuff. However, if someone dials an invalid number, then instead of hearing a "three tone", the line just drops and goes dead. The console

Hello, When I run LLC with option "-O0 -march=sparc" on following testcase, fast register allocator crashes with "UNREACHABLE executed" error. LLC generates code successfully with other standard register allocators available. $ cat call.ll define void @test() nounwind { entry: %0 = tail call i32 (...)* @foo() nounwind tail call void (...)* @bar() nounwind ret void }

Hi R users, I would like to know why these following curve densities don't appear correctly on the histograms. Thank you for your help library(lattice) library(grid) resp <- rnorm(2000) group <- sample(c("G1", "G2", "G3", "G4"), replace = TRUE, size = 1000) histogram(~ resp | group, col="steelblue", panel = function(x, ...){ std

I have the following code that perform hiearchical clustering and plot them in heatmap. __ library(gplots) set.seed(538) # generate data y <- matrix(rnorm(50), 10, 5, dimnames=list(paste("g", 1:10, sep=""), paste("t", 1:5, sep=""))) # the actual data is much larger that the above # perform hiearchical clustering and plot heatmap test <- heatmap.2(y)