similar to: Problem with substr

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

dear members, i would like to write a variable in a plot title (main="") but i don't know the right syntax:(...i tried a lot of different ways without success. here my example: y=30 z=33 for (i in 10:length(tissue)) { png(filename = tissues[i], width = 1024, height = 768, pointsize = 12, bg = "white") gene.graph("ENSG00000115252", rma.affy, gps=list(1:3,

Dear useRs, The seqinR package is a library of utilities to retrieve and analyse biological sequences. A new version of seqinR, seqinR 1.0-7, has been released on CRAN. Here is a summary of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC server is released. Preliminary tests suggest that working with about 100,000

Dear useRs, The seqinR package is a library of utilities to retrieve and analyse biological sequences. A new version of seqinR, seqinR 1.0-7, has been released on CRAN. Here is a summary of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC server is released. Preliminary tests suggest that working with about 100,000

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

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

HI, this is my problem I want to subset this file df, using only unique df$exon printing the line once even if df$exon appear several times: unique(df$exon) will show me the unique exons If I try to print only the unique exon lines with df[unique(df$exon),] -this doesn't print only the unique ones :( could you help? thanks Nat exon size chr start

The "genetics" package for handling single-locus genetic data is now available on CRAN in both source and Windows binary formats. The purpose of this package is to make it easy to create and manipulate genetic information, and to facility use of this information in statistical models. The library includes classes and methods for creating, representing, and manipulating genotypes

The "genetics" package for handling single-locus genetic data is now available on CRAN in both source and Windows binary formats. The purpose of this package is to make it easy to create and manipulate genetic information, and to facility use of this information in statistical models. The library includes classes and methods for creating, representing, and manipulating genotypes

Hi, I'm heaving difficulties with a dataset containing gene names and positions of those genes. Not such a big problem, but each gene has multiple exons so it's hard to say where de gene starts and where it ends. I want the starting and ending position of each gene in my dataset. Attached is the dataset: http://www.nabble.com/file/p21312449/genlistchrompos.csv genlistchrompos.csv Column

Good day, The location of indels can be retrieved from a PairwiseAlignmentsSingleSubject object by using indel. Determining any difference between the two sequences, including substitutions, is not quick nor easy. I suppose that summary displays details of the mismatches, but the variable is of class PairwiseAlignmentsSingleSubjectSummary which has no documented accessors. So, the code to access

Dear Peter, I am running your g.test() with the william's correction but I have a question about the input numbers. These are my data: "Our data are consistent with those obtained using microarray comparative genome hybridization in that we found significantly fewer variants per Mb on the X compared to the autosomal chromosomes (152 versus 336 respectively, G = 93.4, P < 2e-16, df =

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")

Hello, I am new to R and still feeling my way thru it. I am trying to plot the values from this file below on the X-axis of a plot. I have attached the graph to the email...the one i am trying to recreate. Exon start end 5'UTR 22540060 22540121 1 22540122 22540140 2 22540303 22540493 3 22541552 22541565 4 22542373 22542519 5 22544265 22544432 3'UTR 22544433 22544856 I would like to

Hello: I was hoping to get some advice about how to return a tree (basically a linked list -- with each node containing a parent, left, and right node pointers) from a C routine back into R. Each node itself contains several attributes (a double, a char *, an int, and a void * ) Initially I was thinking I could just return to R a SEXP containing a pointer to the Root Node, but then realized

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

Hello everyone, I am not sure if this should go on the general R mailing list (for example, if there is a text mining solution that might work here) or the bioconductor mailing list (since I wasn't able to find a solution to my question on searching their lists) - so this time I tried both, and in the future I'll know better (in case it should go to only one of the two). The task

Hello, I've meanwhile got onechannelGUI running (my OS is windows). I'm trying to use it for the analysis of human exon arrays. I was able to load cel files and run them through affymetrix power tools, to obtain normalized affy data. My next step was trying to find differentially spliced exons. The menu offers to calculate either Midas or splice index scores. However, when I try to use

R-users, I have the following piece of code which I am trying to run on a dataframe (aga2) with about a half million records.  While the code works, it is extremely slow.  I've read some of the help archives indicating that I should allocate space to the p1 and ags1 vectors, which I have done, but this doesn't seem to improve speed much.  Would anyone be able to provide me with advice on

Dear all, I have a string, let's say "testing", and I would like to extract in sequence each letter (character) from it. But when I use substr() I only properly get the first character, the rest is empty (""). What am I getting wrong? For example, I have this code: >>> x <- "testing" k <- nchar(x) for (i in 1:k) { y <- substr(x, i, 1)