Re: [R] strsplit help

() in later runs. If time is an issue, a slightly faster way to do this, after the strsplit() function is: Rumino_Reps_agreeWalign$geneid.prefix - sapply(gene.list, [, 1) Rumino_Reps_agreeWalign$geneid.suffix - sapply(gene.list, [, 2) Jean alison waller wrote on 04/11/2012 08:23:29 AM

[R] strsplit help

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:

[R] can't install plotrix

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

[R] Summarizing For Values with Multiple categories

Hi all, I have some data as follows. Cat1 Cat2 Cat3 COG Counts ABC COG1 10 BD 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-

Re: [R] Summarizing For Values with Multiple categories

Thanks! I tried reading the help for aggregate and can't figure out which form of the formula I am using, and therefore the syntax. I'm getting the below error. aggregate(counts ~ ind, merge(stack(CAT2COG), df, by = 1), sum) Error in as.data.frame.default(x) : cannot coerce class formula

Re: [R] Summarizing For Values with Multiple categories

Yes, I guess I should update. R.version.string [1] R version 2.9.0 (2009-04-17) On 24-Oct-10, at 1:12 AM, Gabor Grothendieck wrote: R.version.string __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

[R] Help reading table rows into lists

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

Re: [R] Help reading table rows into lists

Thanks Gabor and Jeffrey, and thanks for explaining the differences. I think I'll go with Jeffery's as I think I want entries for COGs with no pathway. Alison On 10-Oct-10, at 8:59 PM, Jeffrey Spies wrote: sapply(dat, function(x){ tmp-unlist(strsplit(x, '\t', fixed=T)) out -

[R] colour of label points on a boxplot

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

Re: [R] using sprintf to pass a variable to a RMySQL query

/10 16:01, Uwe Ligges wrote: On 10.03.2010 12:45, alison waller wrote: Thanks Gabor, As I said I would like to use gsubfn, but I am having problems installing it, which I assume are due to some conflict with the current tcltk package Below is the error I got after issuing install.packages

Re: [R] using sprintf to pass a variable to a RMySQL query

, dependencies, available, lib) : package 'tcltk' is not available On 03/09/10 16:26, Gabor Grothendieck wrote: On Tue, Mar 9, 2010 at 7:10 AM, alison waller alison.wal...@embl.de wrote: Hi all, Thanks for help with the paste and sprintf syntax. So I've decided to use paste and or sprintf

Re: [R] using sprintf to pass a variable to a RMySQL query

(). That, and use sep='' to get rid of unwanted space characters. Using paste is also effective for constructs like IN (3,4,5) or IN ('a','b','c') though it can be necessary to nest one paste within another -Don At 2:06 PM +0100 3/8/10, alison waller wrote: Hello, I am using RmySQL and would

[R] using sprintf to pass a variable to a RMySQL query

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?

Re: [R] finding most highly transcribed genes - ranking, sorting and subsets?

gene. Thanks again for any suggestions, Alison -Original Message- From: Martin Morgan [mailto:[EMAIL PROTECTED] Sent: Thursday, December 06, 2007 4:06 PM To: alison waller Subject: Re: [R] finding most highly transcribed genes - ranking, sorting and subsets? Hi Alison -- I'm not sure

Re: [R] finding most highly transcribed genes - ranking, sorting and subsets?

Thanks - great, should have thought of option b) -Original Message- From: Martin Morgan [mailto:[EMAIL PROTECTED] Sent: Friday, December 07, 2007 12:52 PM To: alison waller Cc: [EMAIL PROTECTED] Subject: Re: [R] finding most highly transcribed genes - ranking, sorting and subsets? Hi

[R] finding most highly transcribed genes - ranking, sorting and subsets?

Hello, I am not only interested in finding out which genes are the most highly up- or down-regulated (which I have done using the linear models and Bayesian statistics in Limma), but I also want to know which genes are consistently highly transcribed (ie. they have a high intensity in the