search for: geneset

Dear Sir/Madam, I found your email address and your correspondence with R-users. I hope you could help me with this question about the function "ur.ers" in the package of "urca". It is an improved unit root test (Elliott et al. 1996 Econometrica). Do you know how to extract the value of the test statistic from the output? The only thing I can get is the print-out of all

hi I have vector test. It has 3 elements. I want to join the three into one vector. "Geneset=HSA04910_INSULIN_SIGNALING_PATHWAY-157- 20". how can i do it. > class(test) [1] "character" > test [1] "Geneset=HSA04910_INSULIN_SIGNALING_PATHWAY" "157" [3] "20" Ramya -- Vi...

hi there, I want to write the plots in the pdfs and the details about the graph in a seperate notepad. plot(as.numeric(lapply(resultgenes,length)), main= "Geneset.gene#.bias.test",xlab="Top.Ranked.Genesets", ylab="gene.number.per.geneset") lines(loess.smooth(c(1:1000),as.numeric(lapply(resultgenes,length)), span = 2/3, degree = 1, family = "gaussian", evaluation = 50),col=2, lwd=3) i want this graph in the pdf and so...

Hi, Could you please let me know to use a list in a for loop here geneset is a loop.I am trying to match the names of the list with 1st row of the output. result<- list() for(i in 1:length(output) { result[[i]] <- geneset(which(geneset %n% output[,1])) } Kindly help me out -- View this message in context: http://www.nabble.com/For-loop-tp18163665p18163...

hi I want to compare two list by its names and get the values of that list. can anybody let me know the syntax of comparing the list by their names using a for loop c.genes<- list() for(i in 1:100) c.genes[[1]]<- geneset(which(geneset == tobecampared[i])) } here geneset is a list and also tobecampared is a list Thank you Ramya -- View this message in context: http://www.nabble.com/help-on-list-comparison-tp18240445p18240445.html Sent from the R help mailing list archive at Nabble.com.

The GeneSetCollection class in the Bioconductor package GSEABase extends 'list' > library(GSEABase) > showClass("GeneSetCollection") Slots: Name: .Data Class: list Extends: Class "list", from data part Class "vector", by class "list", dis...

..."CD4PCR.txt",header=TRUE,row.names=1,sep="\t",dec=".",fill=TR UE) x<-as.matrix(data) dim(x) (11,37) =11 genes =37 samples (20 no disease, 17 disease) this code: set.seed(100) y <-c(rep(0,20),rep(1,17)) genenames<-as.character(data$Gene.Symbol) geneset<-as.character(rownames(x)) GSA.obj<-GSA.func(x,y, genenames, geneset, resp.type="Two class unpaired") returns this error: Error in 1:max(ngenes, na.rm = TRUE) : result would be too long a vector In addition: Warning message: In max(ngenes, na.rm = TRUE) : no non-missing argume...

...differential expression is correlated (more power). Hence I want to do a biased permutation, selecting random genes that together follow the same expression level distribution. This is what I've done so far: geneExp is my data.frame with DE statistics. 6585 rows of genes, col one is gene ID. geneSet is my gene set, column one is gene ID. index is the index of the genes DE in my geneExp. dSign=density(geneExp[index,'baseMean']) #baseMean is a measure of expressionlevel prob=lapply(geneExp[,"baseMean"],function(x) approx(dSign$x,dSign$y,x)$y) prob=unlist(prob) So when I am...

Hi, I have an RData file containing a GeneSetCollection object (Bioconductor), http://www.cs.mu.oz.au/~gabraham/c2.RData. I think it uses lazy loading because packages are only loaded when I access the object (see below) in the R console. When I try the same with Rscript, it segfaults. This happens on 2.9.0 both on Linux and Mac: Rscript...

...ss <- sum(rep(1/(N-Ns), sum(ranklist[1:j,2]==0))) if((phit-pmiss)>score[i]) score[i] <- phit - pmiss } } I tried a little bit, but not enough knowledge in C. #include <stdio.h> #include <R.h> #include <Rdefines.h> #include <math.h> SEXP ESscore(SEXP Rgeneset, SEXP Rgenemat, SEXP Rranklist, SEXP sim) { int nc = ncols(Rgenemat); double *geneset = NUMERIC_DATA(Rgeneset); double *genemat = NUMERIC_DATA(Rgenemat); SEXP Rscore; PROTECT(Rscore=NEW_NUMERIC(sim)); double *score = NUMERIC_DATA(Rscore); for(i=1; i<=sim; i++){ if(i>2) {genemat...

Has something changed in R that requires an update in the genetics package by Gregory Warnes? I am using R version 2.5.0 This used to work > summary(founders[,59]) to prove that it is a genotype class > class(founders[,59]) [1] "genotype" "factor" Now when I issue the command: > summary(founders[,59]) I get: Error in attr(retval, "which") <- which :

Geneset_name #Chromosome #Hit_in_Biomart original_geneset_len Missing.genes [1,] "AGUIRRE_PANCREAS_CHR12" "1" "51" "59" "8" [3,] "AGUIRRE_PANCREAS_CHR9&q...