similar to: how to separate char and num within a variable

May I ask a clinical question? For a trial, we have a treatment group of small size, say 30 patients. We want to selectmatching control patients from a bigger group (100 patients) in terms of several clinical variables, such as age, tumor stage etc. This practice is to select the closest matching set of control cases. I wonder if R has any routine or package that can help with this problem.

i'm sorry. i had an error in my previous code because i left out a letter in the rownames. while fixing that, i also found a solution. so i'm sorry for the confusion. below is my fix. temp2 <- matrix(rnorm(10),nc=1,nrow=10) rownames(temp2) <-

Dear all, Does any one know how to remove part of the string? For example, "LTA4H||Leukotriene A4 hydrolase" is a gene name plus gene description. I hope to remove "||Leukotriene A4 hydrolase". What would be the R code to do that using gsub()? Many thanks! Bill

Dear all, Does any one know if any R package or function can do Ordinary Least Products regression? Many thanks! Bill

this is a bad question but I can't figure it out and i've tried. if i sort the 2 column matrix , temp1, by the first column, then things work as expected. But, if I sort the 1 column matrix, temp2, then it gets turned coerced to a vector. I realize that I need to use drop=FALSE but i've put it in a few different places with no success. Thanks. temp1 <-

Hi all, I am given the a data frame in which one of the columns has more information together- see column 4, peak_loc: chr start end peak_loc cluster_TC strand peak_TC 1 chr1 564620 564649 chr1:564644..564645,+ 94 + 10 2 chr1 565369 565404 chr1:565371..565372,+ 217 + 8 3 chr1 565463 565541 chr1:565480..565481,+ 1214 + 15 4 chr1

Hi,? I have two big data set.? data _1 :? > dim(data_1) [1] 15820 5 > head(data_1) ? ?Chromosome ?????Start????????End????????Feature GroupA_3 1: ? ? ? ????????chr1 521369 ?750000 ????chr1-0001 ? ?????0.170 2: ? ? ? ????????chr1 750001 ?800000 ????chr1-0002 ? ????-0.086 3: ? ? ? ????????chr1 800001 ?850000 ????chr1-0003 ? ?????0.006 4: ? ? ? ????????chr1 850001 ?900000 ????chr1-0004 ?

Hi all, In short: I'm running ddply on an admittedly (somehow) large data.frame (not that large). It runs fine until it finishes and gets to the "collating" part where all subsets of my data.frame have been summarized and they are being reassembled into the final summary data.frame (sorry, don't know the correct plyr terminology). During collation, my R workspace RAM usage goes

Hello I have a data frame as below V1 V2 V3 V4 V5 V6 chr1 18884 C CAAAA 2 0 chr1 135419 TATACA T 2 0 chr1 332045 T TTG 0 2 chr1 453838 T TAC 2 0 chr1 567652 T TG 1 0 chr1 602541 TTTA T 2 0 on which I want to perform complex rearrangement such that: if V3 is a string >1 (i.e line 2) then I

Hi Jim I am trying to prepare a bed file to load as accustom track on the UCSC genome browser. I have a data frame that looks like the one below. > x V1 V2 V3 1 chr1 11255 55 2 chr1 11320 29 3 chr1 11400 45 4 chr2 21680 35 5 chr2 21750 84 6 chr2 21820 29 7 chr2 31890 46 8 chr3 32100 29 9 chr3 52380 29 10 chr3 66450 46 I would like to insert the following 4 lines at the beginning:

Hi Peter I have the following data frame with chromosome name, start and end positions: chrN start end 1 chr1 11122333 11122633 2 chr1 11122333 11122633 3 chr3 11122333 11122633 8 chr3 111273334 111273634 7 chr2 12122334 12122634 4 chr1 21122377 21122677 5 chr2 33122355 33122655 6 chr2 33122355 33122655 I would like to count the positions that have the same start and

Hi, I want to merge multiple chromosomal regions based on their common intersecting regions. I tried couple of things using while and if loops but did not work out. I would appreciate if anyone could provide me a small piece of code in R to get the intersection of following example: chr1: 100-150 chr1: 79-250 chr1: 100-175 chr1: 300-350 I want the intersection of all four regions as follow:

Hi, I am given the following table: > head(hsa_refseq) chr genome region start stop nu strand nu.1 nu.2 gene_id 1 chr1 hg19_refGene CDS 67000042 67000051 0 + 0 gene_id NM_032291 2 chr1 hg19_refGene exon 66999825 67000051 0 + . gene_id NM_032291 3 chr1 hg19_refGene CDS 67091530 67091593 0 + 2 gene_id NM_032291 4 chr1 hg19_refGene exon

Hello, I'm a new R user. I have two different dummy tables with the variable name tb1 and tb2. tb1< v1 v2 v3 v4 "chr1" 22 23 3 "chr1" 36 37 1 "chr1" 54 55 0 "chr1" 77 78 1 "chr2" 80 81 4 "chr2" 85 86 0 "chr2" 99 100 1

Hello all, I have written a for loop to act on a dataframe with close to 3million rows and 6 columns and I would like to pass it to apply() to speed the process up (I let the loop run for 2 days before stopping it and it had only gone through 200,000 rows) but I am really struggling to find a way to pass the arguments. Below are the loop and the head of the dataframe I am working on. Any hints

Hi everyone, I am trying to find a way to filter a table; If I am given for example the following table: > head(intra) chr miRNA start end strand ACC hsa_ID region region_start region_end gene_id transcrip_id 1 chr1 miRNA 1102484 1102578 + ACC="MI0000342"; ID="hsa-mir-200b"; exon 1102484 1102578 NR_029639 NR_029639 2 chr1

someone sent in a question earlier about doing something in 3D so i took a stab at it purely for educational purposes ( i'm not even sure that I understood the question actually ). Unfortunately, persp gives me an error that I don't understand because it says "object y not found". I'm sending y in as a parameter to persp similar to what ?persp shows in one of oits examples

Dear all, I have a problem. I have m variables each of which has n observations. I want to calculate pairwise correlation among the m variables and store the values in a m x m matrix. It is extremely slow to use nested 'for' loops if m and n are large. Is there any efficient alternative to do this? Many thanks for your suggestions!! Bill

I do have a bunch of genes ( nearly ~50000) from the whole genome, which read in genomic ranges A range(gene) can be seem as an observation has three columns chromosome, start and end, like that seqnames start end width strand gene1 chr1 1 5 5 + gene2 chr1 10 15 6 + gene3 chr1 12 17 6 + gene4 chr1 20 25 6 + gene5

Hi, Recently added to doc/NEWS.Rd: 'R CMD check' now gives a warning rather than a note if it finds inefficiently compressed datasets. With 'bzip2' and 'xz' compression having been available since R 2.10.0, there is no excuse for not using them. Why isn't a note enough for this? Generally speaking, warnings are for things that are dangerous, or unsafe,