search for: enrichment

Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? Thanks for any comments. best, Tim [[alternative HT...

Hello all, I would like to introduce our group's new bioinformatics package to you: pathfindR <https://cran.r-project.org/package=pathfindR> This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved...

Hello all, I would like to introduce our group's new bioinformatics package to you: pathfindR <https://cran.r-project.org/package=pathfindR> This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved...

...1(119) HIC1(122) TRAPPC3     EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89) RFX(121) ZTA(168) NDUFS5     WHN(14) ATF(57) EGR3(59) PAX5(99) SF1(108) NRSE(146) TIE1     NRSE(129) I would like to test the 2nd column (each value has letters followed by numbers in brackets) here for enrichment via fisher.test. To that end I am trying to create two factors made up of column 1 (Gene) and column 2 (TFBS) where each Gene would have several entries matching each TFBS. My main problem just now is that I can't split the TFBS column into separate strings (at the moment that 2nd column is a...

Dear R users,  I hope you can help me as you have done before.  I was wondering if I can make some of the points on my graph a different colour and symbol? Some of my soil samples are enriched and I wanted them to be shown with a red triangle and the samples which are not enriched I wanted to show with a blue square. I can't seem to find a way of doing this if there is a way?  My script:  

I'd like to pick every imbricated five character long subsets from a vector. I guess there is some efficient way to do this without loops... Here is a for-loop-version and a model for output: VECTOR=c(1,4,2,6,5,0,11,10,4,3,6,8,6); ADDRESSES=c(); for(i in 1:(length(VECTOR)-4)){ ADDRESSES[i]=paste(VECTOR[i:(i+4)],collapse="") } > ADDRESSES [1] "14265"

...;,"Impact"),c("Update knowledge and skills","Meet requirements for current position","Discover new job opportunities","Discover new job opportunities","Transition to a new job","Meet requirements for certificaiton","Personal enrichment","Update knowledge and skills","Meet requirements for current position","Meet requirements for certificaiton","Personal enrichment","Transition to a new job"))) colnames(data)=c("mean","variable","Q") data[,1]=mean...

Hi, I am very new to R and wanted to know if there is a package that, given very long nucleotide sequences, searches and identifies short (7-10nt) motifs.. I would like to look for enrichment of certain motifs in genomic sequences. I tried using MEME (not an R package, I know), but the online version only allows sequences up to MAX 60000 nucleotides, and that's too short for my needs.. Thanks A

I am trying to use the levelplot function from a command file. Here is the code: library(sp) library(gstat) library(lattice) gatherData <- read.table("~/gather.txt", header = TRUE) grd = makegrid(gatherData$x, gatherData$y, cell.size = 5) k <- krige(z~x+y, ~x+y, data = gatherData, newdata = grd, nmax = 5) levelplot(var1.pred~x+y, k, aspect = mapasp(k), main = "Predicted

Hi all, I'm discovering LLVM and I want to build a customized CFG with customized nodes (here BasicBlocks). Simply, the purpose is to enrich CFG with some other informations. What is the best way to do that ? Please, tell me if I'm wrong (I'm not familiar enough with c++) but I understand that : - CFG is a GraphTraits<BasicBlock*> - it's not allowed to inherit from

What am I doing wrong? > install.packages("Hmisc") trying URL `http://cran.r-project.org/src/contrib/PACKAGES' Content type `text/plain; charset=iso-8859-1' length 47565 bytes opened URL ================================================== downloaded 46Kb trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz' Content type `application/x-tar' length

...test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow with the requisite packages? I am trying to find out to fetch GO ontologies for homo sapiens with bioconductor but most packages are designed for enrichment analysis. Am I missing something here? Any help would be greatly appreciated. Thanks a lot in advance. -- Warm Regards, Sandeep Amberkar BioQuant,BQ26, Im Neuenheimer Feld 267, D-69120,Heidelberg [[alternative HTML version deleted]]

Hello I am getting memory allocation errors when running a function that uses locfit within a for loop. After 25 or so loops, it gives this error. "Error: cannot allocate vector of size 281250 Kb" Running on linux cluster with a Gb of RAM. Problem never happens on my OS X (less memory). The total data is 130 cols by 5000 rows The first 129 cols are response variables, the 130th

Dear r-help reader, I have some problems with the aggregate function. My datframe looks like >frame Day Time V1 V2 1 M 0 3 NA 2 M 0 4 NA 3 M 0 5 2 4 M 1 NA 4 5 M 1 10 6 6 T 0 4 45 7 T 1 4 3 8 T 1 3 2 9 T 1 6 1 I used the aggegate function to obtain the mean in V1 and V2 over the grouping variable Time and Day

For example, this station: http://radio.dyne.org:8000/ondarossa.mp3 has got a xspf file? I obtain a message: Could not parse XSLT file when i try to open it For the stations that I can't found in yp.xml (e.g. http://212.162.68.230/1.mp3 http://212.162.68.230/2.mp3 http://212.162.68.230/3.mp3 http://stream15.top-ix.org/ondequadre ) it means they aren't on an official

Hi in order to keep the dial tone after pressing 9 for 'outside line' I have this in my extensions.conf [localpstn] ignorepat => 9 exten => _9[123456789]XXXXXXX,1,Dial,${PSTN}/${EXTEN:1} exten => _9[123456789]XXXXXXX,2,Congestion this is properly included in the handsets' context but the dial tone disappears after pressing 9. am I missing something? thanks in advance

Hi John, thank you for your answer. Sorry if I was not clear ^^' I try to build a RCG (Resource Control Graph) which is a CFG with a weight. In my case, this weight corresponds to the number of heap allocations. Then I want to add this weight to each node (then basic block) of this graph. I think that a CFG is a GraphTraits<BasicBlock*> then I suppose that this RCG will be a

R for Mac Special Interest Group Alog with the forthcoming version 1.2.3 of R a new mailing list has been activated. The list is intended to exchange ideas, impressions, give suggestions etc on the portings of R for MacOS and MacOS X. You can subscribe to the list going to its official page: Go to the list page : http://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac To post a message to

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Hi, Has anyone written code for isotonic regression on ordered rectangular grids? Nathan Nathan Leon Pace, MD, MStat University of Utah Salt Lake City, UT 84132 Office: 801.581.6393 Fax: 801.581.4367 Cell: 801.558.3987 Pager: 801.291.9019 Home: 801.467.2925 [[alternative text/enriched version deleted]]