search for: kegg

Greetings all, I would like to append a 4 digit number suffix to the names of my files for later use. What I am using now only produces 1 or 2 or 3 or 4 digits. ############ for (i in 1:1000) { temp <- (kegg [i,]) temp <- merge (temp, subrichcdt, by="gene") file.name <- paste ("kegg.subrichcdt.", i, ".txt", sep="") write.table(temp, file=file.name) } ####### But I want: "kegg.subrichcdt.0001.txt" "kegg.subrichcdt.0002.txt"...

i don't know perl,but on server site,they give soap:lite using perl , go to--->http://www.kegg.jp/kegg/soap/doc/keggapi_manual.html i want to download data from kegg server ,using R only, how to proceed? & what is mean by SOAP client driver ? also go to http://soap.genome.jp/KEGG.wsdl -- View this message in context: http://r.789695.n4.nabble.com/how-to-download-data-from-soap-server-u...

...ends: since these are on search() In R-devel it seems like func --> NAMESPACE, including Imports: (and other details) --> ?? but not pkgs in Depends: Is this correct or as intended, or is there a better conception to have? This model is from the following: In 2.7.0: > library(KEGG.db) # Imports, Depends AnnotationDbi; KEGG.db is data-only > head(ls(KEGGPATHID2EXTID)) [1] "hsa00232" "hsa00230" "hsa04514" "hsa04010" "hsa04012" "hsa04150" vs. in a package tmpA with a NAMESPACE with Depend: and Imports: KEGG.db and...

As far as I know, the following should work. Can anybody tell me if/where I am going wrong? > packageDescription("KEGG", field="Version") [1] "1.6.4" > require(KEGG, version="1.6.4") Loading required package: KEGG [1] FALSE Warning message: There is no package called 'KEGG', version 1.6.4 in: library(package, character.only = TRUE, logical = TRUE, warn.conflicts = war...

-----Original Message----- From: Robert Gentleman [mailto:rgentlem@fhcrc.org] Sent: Wed 10/12/2008 18:47 To: Legaie, Roxane Subject: Re: Kegg.db with GOstats Hi Roxanne, Can you redirect your question to the mailing list. And, you can find the answer in the mailing list archives... best wishes Robert Legaie, Roxane wrote: > Dear Robert Gentleman, > I am currently working on Streptomyces coelicolor microarray data. >...

Hi all , I am facing some problems with 'ls' command. Whenever I use it I get the following error : ls("KEGG.db") Error in as.environment(pos) : no item called "KEGG.db" on the search list ls("pkgname") Error in as.environment(pos) : no item called "KEGG.db" on the search list and this is true for any package. Can anything be done ? Regards, Anupam Sinha, Gra...

Hi, I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. The following error occurs after this command line below: >pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native = F, same.layer = T, species = "hsa", kegg.dir = "test", out.suffix = "up")) Start tag expected, '<' not found Warning: Parsing test/hsa04510.xml file failed, please check the file! That .xml file is empty, while .png file exists. The issue is th...

...ble. As of about a week ago the help.search function dies when used in the simple help.search("something") usage. The error is Error in rbind(...) : number of columns of matrices must match (see arg 203) After some effort I have traced it down to the annotation packages. I installed GO, KEGG, mgu74[abc]v2 and hgu133plus2 all version 1.7.0 When I move these out of the library directory, help.search() functions correctly again. I have not tracked it any further -- just wanted to know if anyone else had noticed it. Gerard Tromp

...; (these will change over time there I want a variable here). Also these files are in many different directories so I want a way filter out the junk... Anyway I don't believe that this is related to my errors but I mention it none the less. > files_to_test <- list.files (pattern = "kegg.combine") > for (i in 1:length (files_to_test)) { + raw_data <- read.table (files_to_test[i], header=TRUE, sep=" ") + tmpA <- raw_data[,compareA] + tmpB <- raw_data[,compareB] + tt <- t.test (tmpA, tmpB, var.equal=TRUE) + tt_pvalue[i] <- tt$p.value +...

Greetings all, I am getting an error message that is stifling me. Any ideas? > ## Define Directories ## > load_from <- "/home/mcc/Dropbox/abrodsky/kegg_combine_data/" > save_to <- "/home/mcc/Dropbox/abrodsky/ttest_results/" > > ############################### > ## Define Columns To Compare ## > compareA <- "log_b_rich" > compareB <- "Fc_cdt_rich_tot" > > ##########################...

...ation Data (hgu133a) hgu95av2 Affymetrix Human Genome U95 Set Annotation Data (hgu95av2) hgu95av2.db Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) hgu95av2cdf hgu95av2cdf KEGG A data package containing annotation data for KEGG keggorth graph support for KO, KEGG Orthology KernSmooth Functions for kernel smoothing for Wand & Jones (1995) lattice Lattice Graph...

Hi, * I am using read.table command as follow kegg<-read.table("c:/IDs.tab",header =TRUE,quote= "'", sep="\t") * Fragment of file is as follow: ID Pathway 04916 Melanogenesis 04920 Adipocytokine signaling pathway 04930 Type II diabetes mellitus 04940 Type I diabetes mellitus 04950 Maturi...

Dear R gurus I?m trying to use the GSCA package to a series of microarray data (prostate cancer normal vs tumor (29 vs 29 paired)) but I?m running into some problems. I have a matrix (named /data_final/) with 11k rows(genes) and 60 cols (58 samples (29N vs 29T), GO IDs, KEGG IDs). I also have a separate vector GS with the GO IDs mapped to genes (no duplicate genes but multiple IDs per gene like in col 59) However when I try to run: /singleDC(data_final, group=c(1:29,30,58), GSdefList = GS, nperm = 3, permDI=TRUE)/ I get an error/ ?unused argument(s) (permDI=TRUE)?/...

...plines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [9] "base" other attached packages: Rgraphviz geneplotter XML GOstats Category hgu95av2 KEGG multtest xtable "1.11.9" "1.11.8" "0.99-8" "1.6.0" "1.4.1" "1.12.0" "1.8.1" "1.11.2" "1.3-2" RBGL annotate GO graph Ruuid limma ge...

...DB BOVINECHIP.DB FLY.DB PIGCHIP.DB YEASTNCBI.DB BOVINE.DB GO.DB PIG.DB ZEBRAFISHCHIP.DB CANINECHIP.DB HUMANCHIP.DB RATCHIP.DB ZEBRAFISH.DB CANINE.DB HUMAN.DB RAT.DB CHICKENCHIP.DB INPARANOID.DB RHESUS.DB CHICKEN.DB KEGG.DB WORMCHIP.DB Those package templates are just the skeletons of the hundreds of annotation packages that we generate. Of course, each of them contains empty subfolders. Having 'R CMD build' remove those empty subfolders breaks all the tools that make use of those package templates...

...way (from my reading anyways) seemed to be by creating the file "Renviron.site" in the R_HOME/etc directory and adding the variable there. I am interested in opinions from the list, or other suggestions on how to do this. For those who are interested, the package does a lot of parsing of KEGG KGML files, and to speed up calculations I offer advice that they should download a copy of the KGML directory for their organism to their local machine, and I want the package to know where those files are at runtime. Thanks in advance, -Robert Robert M. Flight, Ph.D. University of Louisville B...

...1.7.4" "1.9.21" "0.8-0" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20" "0.9975-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12" "1.11.4" "1.13.6" "1.15.12" graph limma affy affyio Biobase "1.13.6" "2.9.13" "1.13.1...

...1.7.4" "1.9.21" "0.8-0" "1.6-0" GOstats Category Matrix lattice genefilter "2.1.13" "2.1.20" "0.9975-11" "0.14-16" "1.13.8" survival KEGG RBGL annotate GO "2.31" "1.15.12" "1.11.4" "1.13.6" "1.15.12" graph limma affy affyio Biobase "1.13.6" "2.9.13" "1.13.1...

...gt;Loading required package: xtable > >Attaching package: 'xtable' > > > The following object(s) are masked from package:graph : > > label > >Loading required package: multtest >Loading required package: Category >Loading required package: KEGG >Loading required package: hgu95av2 >Warning message: >affycoretools contains no vignette, nothing is added to the menu bar in: >addVigs2WinMenu("affycoretools") > > > sessionInfo() >Version 2.3.1 (2006-06-01) >i386-pc-mingw32 > >attached base packages: &...

...thod is called instead of the correct one, despite that I have Browse[1]> showMethods("summary") Function: summary (package base) object="AnnDbBimap" object="ANY" object="Bimap" object="DBIObject" object="HyperGResultBase" object="KEGGHyperGResult" object="LinearMResultBase" object="ListHyperGResult" object="PFAMHyperGResult" object="SQLiteConnection" object="SQLiteDriver" object="SQLiteResult" Browse[1]> class(gos[[1]]) [1] "GOListHyperGResult" But I...