search for: refseq

...IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN IPI:IPI00019922.5|SWISS-PROT:Q8N0Y2-1|TREMBL:Q53F81|ENSEMBL:ENSP00000338860;ENSP00000375594|REFSEQ:NP_060807|H-INV:HIT000028861|VEGA:OTTHUMP00000078377 Tax_Id=9606 Gene_Symbol=ZN IPI:IPI00647423.2|SWISS-PROT:Q8N819-1|REFSEQ:NP_001073870|VEGA:OTTHUMP00000076687 Tax_Id=9606 Gene_Symbol=FLJ40125 Isoform 1 of IPI:IPI00219000.2|SWISS-PROT:P27658|TREMBL:Q53XI6|ENSEMBL:ENSP00000261037|REFS IPI:IPI00291...

I have a data frame that looks like this: > gctablechromonly[1:5,] refseq geometry gccontent X60_origin X60_terminus length kingdom 1 NC_009484 cir 0.6799 1790000 773000 3389227 Bacteria 2 NC_009484 cir 0.6799 1790000 773000 3389227 Bacteria 3 NC_009484 cir 0.6799 1790000 773000 3389227 Bacteria 4 NC_009484 cir...

Dear list, I am having a set of human oligo ids (H200006022 H200002025 H300004703 H200000442 H200005719 H300018350) which I want to map to Ensembl or RefSeq. I am sure R has a function to do that. I downloaded the {oligo} package and tried to use the probeNames function. Although the factor of ologo ids is an object (as the argument to probeNames should be) I retrieve the following error: probeNames(significant_genes[,1]) Error in function (classes, f...

...ote: > On Mon, May 19, 2008 at 10:47 AM, Eleni Christodoulou > <elenichri@gmail.com> wrote: > > Dear list, > > > > I am having a set of human oligo ids (H200006022 H200002025 H300004703 > > H200000442 H200005719 H300018350) which I want to map to Ensembl or > RefSeq. > > I am sure R has a function to do that. I downloaded the {oligo} package > and > > tried to use the probeNames function. Although the factor of ologo ids is > an > > object (as the argument to probeNames should be) I retrieve the following > > error: > > pro...

...DEAD/H box polypeptide 11 like 1DEAD/H box polypeptide 11 like 3DEAD/H box polypeptide 11 like 9 ;; [Source:UniProtKB/TrEMBL;Acc:B7ZGX0] gene ENSG00000227232 1 -1 14363 29570 17551 29343 WASH5P WAS protein family homolog 5 pseudogene (WASH5P), non-coding RNA [Source:RefSeq DNA;Acc:NR_024540] gene ..... Chers list (chersList) name chr start end cellType antibody features maxLevel score chr1.cher1 1 859132 859732 human AB ENSG00000223764 ENSG00000231958 ENSG00000187634 1.25736038968316 0.664381383074449 chr1.cher2...

> chromosomes id refseq name length 1 0 NC_000001.9 Homo sapiens chromosome 1 247249719 2 1 NC_000002.10 Homo sapiens chromosome 2 242951149 3 2 NC_000003.10 Homo sapiens chromosome 3 199501827 4 3 NC_000004.10 Homo sapiens chromosome 4 191273063 5 4 NC_000005.8 Homo sapiens chrom...

Sorry about this one being long, and I apologise beforehand if there is something obvious here that I have missed. I am new to creating my own functions in R, and I am uncertain of how they work. I have a data set that I have read into a data frame: > gctable[1:5,] refseq geometry X60_origin X60_terminus length kingdom 1 NC_009484 cir 1790000 773000 3389227 Bacteria 2 NC_009484 cir 1790000 773000 3389227 Bacteria 3 NC_009484 cir 1790000 773000 3389227 Bacteria 4 NC_009484 cir 1790000 773000 3389227 Bacteria 5...

.... Can anyone suggest an approach to accomplish this? An additional though less significant question is how I can get the panels to be in the order of the chromosomes as listed in the chromosomes table rather than alphabetical order of their names. thanks Dan > chromosomes chromosome refSeq name length 1 0 NC_000001.9 Homo sapiens chromosome 1 247249719 2 1 NC_000002.10 Homo sapiens chromosome 2 242951149 3 2 NC_000003.10 Homo sapiens chromosome 3 199501827 4 3 NC_000004.10 Homo sapiens chromosome 4 191273063 5...

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

...e.g., linear models, machine learning, and other multivariate analysis methods. * Programming experience and ability to write R and Perl script. * The candidate will have experience with large-scale genomics data and a solid understanding of bioinformatics data bases (eg: GenBank, RefSeq, dbSNP etc) * Experience with some bioinformatics software such as: Spotfire, Partek, Ingenuity, GeneGo, Balst, and Blat. * The candidate will have the ability and interest in learning new techniques and skills in accordance with evolving research program needs. * Candida...

...RaGene-1_0-st-v1.r4.clf" > pgfFile <- "RaGene-1_0-st-v1.r4.pgf/RaGene-1_0-st-v1.r4.pgf" > pkg <- new("AffyGenePDInfoPkgSeed", author="Anne-Marie Madore", email="anne-marie.madore.1@ulaval.ca", version="0.0.1", + genomebuild="RefSeq April 3, 2007, GenBank® January 25, 2007, Rat Ensembl transcripts April 3, 2007 ", + biocViews="AnnotationData", pgfFile=pgfFile, clfFile=clfFile, transFile=transFile, probeFile=probeFile) > makePdInfoPackage(pkg, destDir=".") Creating package in ./pd.ragene.1.0.st.v1...

I want to take the first row of each unique ID value from a data frame. For instance > ddTable <- data.frame(Id=c(1,1,2,2),name=c("Paul","Joe","Bob","Larry")) I want a dataset that is Id Name 1 Paul 2 Bob > unique(ddTable) Will give me all 4 rows, and > unique(ddTable$Id) Will give me c(1,2), but not accompanied by the name column.