similar to: GO & Protein Complex Analysis for Homo sapiens

Hello, I am exporting a graph in "gml" format from igraph 0.5.5. When I open the file in Cytoscape v.2.7 I can't map the color attribute that I assign to the graph when I export it from igraph. Could anyone help me in this? Thanks. -- Warm Regards, Sandeep Amberkar BioQuant,BQ26, Im Neuenheimer Feld 267, D-69120,Heidelberg Tel: +49-6221-5451354 [[alternative HTML version

Hello Everyone! This is my first post to the mailing list so please forgive me if I am a bit deflected from the general format of this mailing list posts. Since I need help in this matter urgently, I would cover up any of my mistakes in posting later. That said, I have a problem in merging 2 graphs that have common nodes between them. I have a graph G1, that have nodes N1 and edge set E1 and

> 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 chromosome 5 180857866 6 5 NC_000006.10 Homo sapiens chromosome 6

Through converting a miRNAs file from FASTA to character format I get a vector which looks like the following: > nml [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7b MIMAT0000063 Homo sapiens let-7b" [3] "hsa-let-7c MIMAT0000064 Homo sapiens let-7c" [4] "hsa-let-7d MIMAT0000065 Homo sapiens

I have the following vector of strings (shown only the first 3 elements) > desc[1:3] [1] "hsa-let-7a MIMAT0000062 Homo sapiens let-7a" [2] "hsa-let-7a* MIMAT0004481 Homo sapiens let-7a*" [3] "hsa-let-7a-2* MIMAT0010195 Homo sapiens let-7a-2*" > is.vector(desc) [1] TRUE > A <- unlist(strsplit(desc[1:3], " ")) > A [1]

Hi ALL, I have very simple question regarding pattern matching. Could anyone tell me how to I can use R to retrieve string pattern from text file. for example my file contain following information SpeciesCommon=(Human);SpeciesScientific=(Homo sapiens);ReactiveCentres=(N,C,C,C,+ H,O,C,C,C,C,O,H);BondInvolved=(C-H);EzCatDBID=(S00343);BondFormed=(O-H,O-H);Bond+

On 13 October 2015 at 16:41, Rafael Espíndola <llvm-dev at lists.llvm.org> wrote: >> - *Be welcoming.* We strive to be a community that welcomes and supports >> people of all backgrounds and identities. This includes, but is not limited >> to members of any race, ethnicity, culture, national origin, colour, >> immigration status, social and economic class, educational

Hi, Am am plotting aggregated frequency data (extracted from an RDBMS) relating to DNA sequence features for each of the human chromosomes as described in the table chromosomes below (the frequency data is in a table 'hits' that has a value (or not) for each of a set of bins across each chromosome). I would like to mark the extent of the chromosome (according to the length value in

Hi R-users, I have a dataset like this: kuvaaja kuva yhteispisteet Hannu isokala 8 Hannu kaapin alta löytynyt 2 Hannu kaapin alta löytynyt 2 8 Hannu limamikko 1 Hannu maukasta marmeladia 8 Hannu skrinnareita 4 Hate madekoukkujen suojelupyhimys 3 Hate matka aikaan joka ei enää palaa 3 Hate munat puoliks padassa 6 Hate pyynikki 2 Hate vailla armeerausta 2

Hi R-users, I have a data frame like this: photographer category picture points Hannu kalat limamikko 1 Teemu kalat verkkovaja 3 Hate kalat munat puoliks padassa 6 Hannu kalat isokala 8 Teemu kasvit, sienet ja muut eliöt harppi 2 Hate kasvit, sienet ja muut eliöt pyynikki 2 Petteri kasvit, sienet ja muut eliöt harmaaleppä 5 Lauri kasvit, sienet ja muut eliöt lumipuu 9 Teemu linnut kainostelua 1

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

Are there any R packages to import and use Web Ontology Language (OWL) ontologies (represented in OWL/RDF or other form)? Thanks, -s [[alternative HTML version deleted]]

Dear all, I have data.frame object in R. I want to export it in tab-delimited file with several lines of header initiated with comment sign (#). I do not know how to do that in R. Could you please give helps on this problem? Thanks in advance. Best, Jian-Feng, ################################################################## The lines I want to write in the header lines look like, with words

Hi: I have clustered microarray gene expression data and trying to map between microarray probe, gene, pathway, gene ontology, and homology for a set of (affy) microarray probes. Is there any package in R which facilitates this? I am looking at bioconductor, but till now could not find a solution. A link to some worked example would be appreciated. Thanks and regards. John [[alternative HTML

our group at Duke is currently attempting to connect two data sets fed through a web-based system, one containing research questions (i.e., variables positioned with certain roles) and a database of statistical methods. this connection is done informally in a number of R packages and related software such as Rcmdr, R4calc, and Rkward where a variable of a certain type is matched to a certain

Dear R experts, I try to extract certain child nodes from an XML document and construct a table in which the parent node names are the columns and the child id values, joined in a list, are the cell content. If I first apply an XPath query to extract all above parent nodes, then iterate over those nodes and again apply a XPath query to select their child nodes, I get *ALL* matching child nodes

Dear R Help Members, I need to draw a pie chart for someone and there are 3 small slices in it identifying different species, all 0.7%, who’s labels overlap so you cannot read them. Is there a way to have only 1 label the three slices, so as to merge the three labels into one without merging the 3 slices? Alternatively, is there a way to extend the pointing lines, so that they could be different

Hi everyone, I''m using a svn pre-commit hook to check manifests for syntax errors. I''ve recently upgraded puppet from 0.22.4 to 0.23.2 and the hook stopped working. I use the following command to parse .pp files: /usr/local/bin/puppet --confdir=/tmp --vardir=/tmp --parseonly --ignoreimport /tmp/$$.pp Now, I make a decision based on the exit code. If 0 then commit, else exit

Dear all, I have a data which is in text file and i would like to import the data to R. From the manual, i?ve found the read.table command function is the most appropriate but when i wrote the command an error had occur. It say ?Error in read.table"C:/Users/user/Documents/cfa-1.txt", header = T, sep = "\t",skip=10) :more columns than column names?. Please help me with this as

Hello, I've read in a data file as a frame and now I'd like the columns to be rows and the rows to be columns. What's the easiest way to do this in R? > class(d) [1] "data.frame" > rownames(d) [1] "98x101" "40x98" "30x40" "0x30" > colnames(d) [1] "H..sapiens" "C..elegans"