similar to: finding most highly transcribed genes - ranking, sorting and subsets?

Hi all, I have a large table mapping thousands of COGs(groups of genes) to pathways. # Ex COG0001 patha pathb pathc COG0002 pathd pathe COG0003 pathe pathf pathg pathh ## I would like to combine this information into a big list such as below COG2PATHWAY<- list (COG0001 = c ("patha ","pathb ","pathc

Hi all, I have 6 datasets(dataframes Assem_ContigsLen7 through all_ContigsLen12) containing 3 columns (contig_id, contig_length, read_count). Each dataset is composed of 3 types of contigs (assemblies of genomic fragments), 1- all Bacterial fragments, 2 - all Viral fragments, 3 - mixed fragments. I identified the type of contig through a merge with another table with just contig_id and

Hi all, I'm having problems installing plotrix. I tried installing it through install.packages, and from the unix command line, but each time it seems to stall when it is installing the help indices. has anyone had this same problem, is this package still maintained ? any help? thanks > install.packages("plotrix") > > I also tried using the source package > R CMD

Hello, I am using RmySQL and would like to iterate through a few queries. I would like to use sprintf but I think I'm having problems mixing and matching the sprintf syntax and the SQL regex. I have checked my sqlcmd and it works when I wan to match %MG1% but how do I iterate for i 1-72? Escape characters,? thanks in advance i<-1 sqlcmd_ScaffLen<-sprintf('SELECT scaffold.length

Hi all, I have some data as follows. Cat1 Cat2 Cat3 COG Counts A B C COG1 10 B D COG2 20 C COG3 30 D COG4 40 I would like to sum all the counts for each category: A B C D 10 30 40 60 >CAT2COG<-

Dear all, I want to use string split to parse column names, however, I am having some errors that I don't understand. I see a problem when I try to rbind the output from strsplit. please let me know if I'm missing something obvious, thanks, alison here are my commands: >strsplit<-strsplit(as.character(Rumino_Reps_agreeWalign$geneid),"\\.") >

I have seen lots of companies offering this as a service and have used phonetag.com in the past. They work very nicely, however I have a customer that is not interested in paying $30-$40 a month but would rather buy the software. I have googled and googled all I can come up with are companies that do it as hosted. Does anyone on the list know of software that can transcribe an email/voicemail

Dear Debian persons I would like enquire about whether the repository deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/ I tried to follow the instructions and I cannot get R3.5.1 - I get R3.4.4??? I have been able to install R3.5.1 on Ubuntu 16.02 using the xenial-cran35/ repository & so not sure if the bionic link is up to date? thanks in advance Regards Alison

Has anyone had success building a package on a windows machine? I am trying the following command with no luck (perhaps my flags are incorrect?). At this point I am stuck. Any help greatly appreciated. Niels Waller (BTW - I have no idea why it cannot find sh.exe since I have it is a directory that is specified in a path statement) H:\R\bin>rcmd build --binary --use-zip h:\taxon2 * checking

I have written an R function that writes output to an external file using the sink function. I assume that `sink' is not operating system dependent. At the end of the function I have additional code that opens the newly created file using notepad on a Windows system. Obviously, this part of the code will not work on a Mac or Linux box. Since I do not have a machine with Linux or the Mac OS

Is R behaving correctly in this example? I do not understand why column 2 has any 2s in it (and why column 3 has any 1s) > x<-matrix(0,10,3) > x[seq(1,10,by=2),2:3]<-c(1,2) > x [,1] [,2] [,3] [1,] 0 1 2 [2,] 0 0 0 [3,] 0 2 1 [4,] 0 0 0 [5,] 0 1 2 [6,] 0 0 0 [7,] 0 2 1 [8,] 0 0 0 [9,] 0 1

R colleagues, I am stumped. I would like the inter-tick distances to be the same on the x and y axes but cannot determine how to do so when the lower half of the y axis is not printed. Thanks for any and all suggestions. (btw, setting par(pty="s") does not solve my problem) Niels Waller M<-matrix(c(2,1, -1,3),2,2,byrow=TRUE)

Hi, I guess this might be a FAQ or something, and there's probably a nice simple way to do it, but I can't think of it: Given a matrix, I want to remove columns that are _entirely_ filled with NAs (partial NAs are fine). How please? Thanks, Martin

Hello all, I am trying to use the micEcon 'insertRow' function inside a function I have written. For example: insert_row_test <- function(m){ insertRow(m,nrow(m)+1,v=0,rName="test") } However, when I try to call the 'insert_row_test' function (after loading the micEcon package), it does not insert a row into the matrix I pass in. When I call the insertRow

Hi, I have a table with data, as below: dput(table): structure(list(Adrian.Cole = c(0L, 0L, 0L, 0L, 0L, 0L), Alison.Wong = c(0L, 0L, 0L, 0L, 0L, 0L), Andrei.Savu = c(0L, 0L, 0L, 0L, 0L, 0L), Bruno.Dumon = c(0L, 0L, 0L, 0L, 0L, 0L), Edward.J..Yoon = c(0L, 0L, 0L, 0L, 0L, 0L), Eugene.Koontz = c(0L, 0L, 0L, 0L, 0L, 0L), Jakob.Homan = c(0L, 0L, 0L, 0L, 0L, 0L), Kelvin.Kakugawa = c(0L, 0L,

Hi, I''m trying to setup my mongrel clusters to start on boot. I have followed the instructions under the "On Boot Initialization Setup" section at http://mongrel.rubyforge.org/docs/mongrel_cluster.html. When I try to start it up, I get the following error: me at mybox.com: sudo /etc/init.d/mongrel_cluster start Starting all mongrel_clusters... !!! Path to log file not

Hello all, I am trying to use cbind to add a named empty column to a Matrix: outputmatrix <- cbind(outputmatrix,kog_id = seq(0,0,0)) The problem I have is that kog_id is a variable that has a value e.g. "KOG1234", but I when I try to use this to name the added column, it is named literally "kog_id" instead of "KOG1234". How can I name a column by passing in a

Dear R community, I am running R 2.0.1 on a Windoze XP OS. I recently upgraded from R 1.9x to 2.0.1 and I am currently upgrading a my personal function packages. My other packages compiled without a hitch but I am having a difficult time with my largest package. Can someone please help me with the following error message "Error in parse(file, n, text, prompt) : syntax error on line

On 18/12/2019 21:49, Eric Christopher wrote: > Yes, I looked through those sources and a number of my questions > around which clang versions have been supported and directory > structure. I think the only difference is removing the direct > questions about earlier flang, but I still don't see code generation > or uses of llvm libraries that would conform to "written in

Hello all, I have generated a principal components regression model using the pcr() function from the PLS package (R version 2.12.0). I am getting a "non-conformable arguments" error when I try to use the predict() function on new data, but only when I try to read in the new data from a separate file. More specifically, when my data looks like this #########training data