[R] converting a character string to an object name

I am trying to automate the way i read my tables. I have an Excel sheet I'm reading using openxlsx package. The sheet contains over 30 sheets, i would like to save each of them as separate objects. my workflow for now is as such: wb <- loadWorkbook(xlsxFile = "Output/Up_Down_Regulated_Gene_Lists.

[R] install lapack for mac

Hi, I am running R under Rstudio for the analysis of single-cell RNA-Seq data. When trying to analyse some data I keep getting the message > slicer_traj_lle <- lle(t(deng[slicer_genes,]), m = 2, k)$Y finding neighbours calculating weights Error in eigen(G, symmetric = TRUE, only.values = TRUE) :

[R] convert a text file into a list (of lists)

Hi, I have a text file i would like to read into a list structure in R. the files is something like that (which might be describe as a list of data frames): [[1]] NAME MEM.SHIP FBgn0037415 FBgn0037415 0.8035441 FBgn0010812 FBgn0010812 0.6579683 FBgn0265351 FBgn0265351 0.64433

Re: [R] subsetting a data.frame based on a specific group of columns

3 > 1 1232 357 23 0 9871 72 > 20 00 811 795 743 > 3 43 919 00 0 > > > Jim Holtman > Data Munger Guru > > What is the problem that you are trying to solve? > Tell me what you want to do, not how you want to do it. > > On Fri, Nov 6

[R] subsetting a data.frame based on a specific group of columns

Hi, I have a data frame with multiple columns, which are belong to several groups like that: X1X2X3Y1Y2Y3 1232357230987172 0719811795743 4391907614 I would like to filter such rows out, where the sums in one group

[R] converting a data.frame into a different table

Hi, I have a matrix of 4.5Kx4.5K elements with column- and row names I need to convert this matrix into a table, where one column is the name of the row for the element, the second column is the name of the column for the same element and the third column is the element itself. The way I do it a

[R] extract duplications from list

Hi, I have a list of 40 data.frames. I would like to identify duplicated entries in the whole list, not only in one specific data.frame, but in all 40. Here is my list: > myList [[1]] XNAME MEM.SHIP 1 FBgn008 FBgn008 0.9304502 2 FBgn014 FBgn014 1.000 3 F

[R] bin a vector of continuous variables

Hi all, I have a data.frame of three columns: partner1 partner2 Substract 1_5000_5001_1 1 5001 2282.3435 1_5000_10001_15000110001 174.1275 1_5000_15001_2115001 273.822 1_5000_20001_25000120001 546.27

Re: [R] DanteR problems

What's that suppose to mean? Do you always expect problem when you do something? On Thu, Jan 9, 2014 at 12:11 PM, Patrick Burns wrote: > On 09/01/2014 10:41, Assa Yeroslaviz wrote: > >> Hi, >> >> I am trying to run the DanteR package, but keep getting some pr

[R] DanteR problems

Hi, Iam trying to run the DanteR package, but keep getting some problems. I installed the Gtk 2.24 version on my mac and was able than to install the RGtk2 package and load it. After installing the DantR package I tried to load it but I keep getting strange error massages. > library(DanteR); da

Re: [R] gsub semicolon with double quotation mark

vector. But I think that is not what you're trying to do. Are you > trying to split the column into three different columns? If so you can > look at the colsplit function in the reshape2 package. > > Best, > Ista > > On Tue, Jan 24, 2012 at 8:18 AM, Assa Yeroslaviz wro

Re: [R] gsub semicolon with double quotation mark

our solution works fine, but I would like to do it for the complete column. I was trying ti use apply on the column, but I get no output. Do you have another idee? Thanks Assa On Tue, Jan 24, 2012 at 13:11, Ista Zahn wrote: > Hi Assa, > > On Tue, Jan 24, 2012 at 6:30 AM, Assa Yeroslaviz w

[R] gsub semicolon with double quotation mark

Hi, I would like to substitute a semicolon with two double quotation marks and a comma inbetween. It suppose to look like that: I have: FBpp0070086;FBpp0099643;FBpp0112915 I would like to have: "FBpp0070086","FBpp0099643","FBpp0112915" I tried with various numbers of backslashes, but noe have wo

[R] libpng warning: Application built with libpng-1.2.26 but running with 1.5.2

Hi, I have a problem on my mac when trying in R to produce png images. I am getting this warnings with the ArrayQualityMetrics package: > arrayQualityMetrics(rma_fatBody, outdir="normData", force =T) The report will be written into directory 'normData'. KernSmooth 2.23 loaded Copyright M. P. Wan

Re: [R] [BioC] comparing two tables

) but it doesn't seems to work at all. Thanks for the help anyway Assa On Wed, Oct 26, 2011 at 15:33, Steve Lianoglou < mailinglist.honey...@gmail.com> wrote: > Hi, > > On Wed, Oct 26, 2011 at 8:17 AM, Assa Yeroslaviz wrote: > > Hi David, > > > > your

Re: [R] [BioC] comparing two tables

is also something to do with bioc as it deals with chromosome regions. But anyway, I think you were right about it.) On Tue, Oct 25, 2011 at 18:01, David Winsemius wrote: > > On Oct 25, 2011, at 10:40 AM, Assa Yeroslaviz wrote: > > Hi all, >> >> @Martin - thanks for the

Re: [R] [BioC] comparing two tables

e queries I get TRUE: > inregion(genetable[3, ], loctable[, c("Start", "End")]) [1] TRUE Do you have Idea, as to how I can fix this problem? Thanks and again sorry for the trouble. Assa On Tue, Oct 25, 2011 at 15:48, Martin Morgan wrote: > On 10/25/2011 03:42 A

[R] comparing two tables

Hi everybody, I would like to know whether it is possible to compare to tables for certain parameters. I have these two tables: gene table name chr start end str accession Length gen1 4 646752 646838 + MI0005806 86 gen12 2L 243035 243141

[R] samr - extract genes from siggenes.table

Hi BioC user, I have a problem extracting the gene set I would like to work with. Here is I work with my data: normData <- read.delim("normalizedData.txt",sep ="\t") # two class unpaired comparison # y must take values 1,2 classes <- c(-1,-2,1,2) #prepere the data for the samr analysis

[R] drosophila2cdf in simpleaffy / affyQCReport

Hi everybody, I have a problem when trying to do the quality control with the packages simpleaffy and affyQCReport with the drosophila chip 2.0 At first I got the messeage, that the *.qcdef file is not there. I followed the instructions in tha manual and created the file like that: array drosoph

Re: [R] ROCR predictions

; > The only information we get from your table is that p-value has small and > continuous values. From what I see the p-values could also be fitting errors > of the predictions (e.g. expressed as a probability that the similarity to > the predicted class is random). > > Claudia &

Re: [R] ROCR predictions

Dear Claudia, thank you for your fast answer. I add again the table of the data as an example. Protein ID Pfam Domain p-value Expected Is Expected True Postive False Negative False Positive True Negative NP_11.2 APH 1.15E-05 APH TRUE 1 0 0 0 NP_11.2 MutS_V 0.0173 APH FALSE 0 0 1 0

[R] ROCR predictions

Hi everybody, I am having a problem building a ROC curve with my data using the ROCR package. I have 10 lists of proteins such as attached (proteinlist.xls). each of the lists was calculated with a different p-value. The goal is to find the optimal p-value for the highest number of true positives

Re: [R] random sample from arrays

r(i in c(1:50)){ >set[i,] <-sample(x,11) > print(c(i,"->", set), quote = FALSE) > } > > run perfectly fine on my computer. > Cheers > > > On Fri, Jul 9, 2010 at 3:10 PM, Assa Yeroslaviz wrote: > > Hi Joris, > > I guess i did it wrong

Re: [R] random sample from arrays

t about the loop altogether and do : > > set <- replicate(11,sample(x,50)) > or > set <- t(replicate(50,sample(x,11))) > > cheers > > On Thu, Jul 8, 2010 at 8:04 AM, Assa Yeroslaviz wrote: > > Hello R users, > > > > I'm trying to extract random sampl

Re: [R] transformation of data.frame

n2 > > > 7 6417 gen3 > > > 8 16070 gen4 > > > 9 6511 gen4 > > > > aa<-lapplyBy(~ID, data=ddd, > > > + FUN=function(uu){ > > > + list(uu$ID[1], paste(uu$gen, collapse=":")) > > > + }) > > > > > > > &

Re: [R] transformation of data.frame

Thanks it works very nicely Assa On Thu, Jul 8, 2010 at 11:15, Petr PIKAL wrote: > Hi > > r-help-boun...@r-project.org napsal dne 08.07.2010 10:45:04: > > > Hello all R users, > > > > I have a problems transforming (or maybe better regrouping) a > data.frame. > > I have a big data.frame, which

Re: [R] transformation of data.frame

gt; 7409 7409 "Gen1:gen3" > 6511 6511 "gen2:gen4" > 6417 6417 "gen3" > > Regards > Søren > > > > > > -Oprindelig meddelelse- > Fra: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] På > vegne af

[R] transformation of data.frame

Hello all R users, I have a problems transforming (or maybe better regrouping) a data.frame. I have a big data.frame, which I would like to sum up according to a specific column. This is an example of my matrix: IDgen 0042787gen2 0016070gen2 0016070gen3 0007409Gen1 0007409

[R] random sample from arrays

Hello R users, I'm trying to extract random samples from a big array I have. I have a data frame of over 40k lines and would like to produce around 50 random sample of around 200 lines each from this array. this is the matrix ID xxx_1c xxx__2c xxx__3c xxx__4c xxx__5T xxx__6T xxx__7T xx

Re: [R] unqiue problem

o you want to use non-unique > entries as rownames? Do you really need the row names, or should you > only be keeping unique values for the first column? > > On Mon, Jun 14, 2010 at 8:54 AM, Assa Yeroslaviz wrote: > > Hello everybody, > > > > I have a a matrix of 2 colu

[R] merging data frames

Hi, is it possible to merge two data frames while preserving the row names of the bigger data frame? I have two data frames which i would like to combine. While doing so I always loose the row names. When I try to append this, I get the error message, that I have non-unique names. This although

[R] adding column of ordered numbers to matrix

Hello everyone, I have a matrix of over 4 line and about 30 columns. For my analysis I would like to add another column with ascending numbers (column header should be "order", and than 1,2,3,4 the end of the matrix). During my analysis I reorder them ( due to merge commands by a differen

[R] Filters()

Hello, I was wondering whether there is a possobility to add File types to the list of filters known by R. I'm using the function choose.files in Windows. I have some files I always use and i would like to filter my option to these kind of files. I have some "atr", "cdt", "gct", "gmt" etc. Is th

Re: [R] paste two columns of a matrix by rows

THX, it's working now. On Wed, May 12, 2010 at 13:54, jim holtman wrote: > Have you tried: > > combined[,19] <- paste(combined[,19], combined[,20], sep=' ') > > On Wed, May 12, 2010 at 4:40 AM, Assa Yeroslaviz wrote: > >> Hello, >> >>

[R] paste two columns of a matrix by rows

Hello, I'm trying to paste two columns of a matrix GB_ACCGENEGENE_SYMBOL NM_010657NM_010657 NM_027162NM_027162 NM_198863NM_198863 NM_010727NM_010727 These two column are a part of a 41,000 x 26 matrix. I wanted these two column to be pasted into one (the firstone, GB_ACC)

Re: [R] comparing and combing files

.txt', header=TRUE, sep='\t', as.is=TRUE) > x2 <- read.table('/tmp/list2.txt', header=TRUE, sep='\t', as.is=TRUE) > combined <- merge(x1, x2, by.x="Probe.Id", by.y="Probe.ID") > Unfortunately your data did not have any IDs i

[R] comparing and combing files

Hello, I have two tab-delimited files which I would like to combine. In the first one I have gene IDs (Unique) on column 1 and than various experimental results from microarray analysis (see attached files list1 ) the second arrays have the same genes IDs (more and in a different order, some are

[R] Rd files must have a non-empty \title

Hello everybody, I'm trying to install a package I have built. This package contains three scripts with various functions (S3 as well as S4 classes) I run at first the package.skeleton command with: > package.skeleton("affyAnalysis", namespace=TRUE, code_files =c("defS3.R", "defS4.R", "qc.R"))

[R] useGeneric and useMethod

hi all, I would like to know what the difference between creating a function using useGeneric and useMethod I'm new to this and would like to know where there is a good documentation about creating my own functions THX, Assa -- Assa Yeroslaviz Kockelsberg 22 51371 Leverkusen Sent

[R] objects masked from packages

dear all, I have a problem with a masked object in a package we created here. we make a package for a workflow of internal analysis of microarray data. to create the package we used: > install.packages(pkgs="affyAnalysis", repos=NULL) > R CMD INSTALL affyAnalysis Erzeuge Verzeichnisse ... Erzeu

[R] setting different environments

Hallo, I have a set of S4 and S3 classes together in one script. While running this script I create a lot of new functions and objects An example for S3 and S4 classes: ## S3 classes pt <- list(x=1,y=2) class(pt) <- "xypoint" xpos <- function(x, ...) UseMethod("xpos") xpos.xypoint <- function(x) x

[R] changing titlessymbols in plot.spm

old1","dodgerblue2","indianred3","lightskyblue","hotpink4"), col.areas = FALSE, col.symbols =unclass(stress.Factor) ,zoom=c(1,5),col.size=2) Unfortunately it's not working. What i get is to see in the attachment. i have two symbols but for the wrong ex

[R] Antwort: FW: R loops

d the help over the net regards for loops in R is quite rare. I'm really thankful for every help. Mit freundlichen Grüßen / Best Regards Assa Yeroslaviz "Richard Pugh" <[EMAIL PROTECTED]> 09.10.2008 14:06 An <[EMAIL PROTECTED]> Kopie Thema FW: [R] R loops

[R] R loops

loop to make in each round a list of the files with the pattern in the directory I'm looking in. what am i doing wrong? If I doing it for each element I'm getting the correct list. THX for the help Best Regards Assa Yeroslaviz [[alternative HTML version deleted]] __