similar to: object is not subsettable

Hi All, I wonder if there should be one character for quote= in read.table, i.e., > args(read.table) function (file, header = FALSE, sep = "", quote = "\"'", dec = ".", ... I have a file containing the following lines, 08248-GOTERM 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process 08279-GOTERM 3'-phosphoadenosine

The following looks like an 'eapply' bug to me: t/subtest> e <- new.env() t/subtest> e$tempo <- quote( 1+'hi') t/subtest> lapply( ls( e), function( x) length( get( x,e))) [[1]] [1] 3 # seems reasonable-- e$tempo is a 'call' object of length 3 t/subtest> eapply( e, length) Error in 1 + "hi" : non-numeric argument to binary operator

eapply() works on most environments, but not on baseenv(). For example, > x <- 1 > eapply(globalenv(), function(x) x) $x [1] 1 > eapply(baseenv(), function(x) x) list() I'm probably not going to have time to work on this before 2.3.0, but I don't think it's really urgent; if no one else fixes it first I'll do it after the release. Duncan Murdoch

Dear R People: I want to get the class of all of the objects in my directory. I was trying: do.call(class,list=ls()) but got an "unused argument error". I'm sure it's simple, but I'm just not seeing it. Any help would be much appreciated. Sincerely, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston -

Hello there, any ideas on how to save all the objects on my workspace inside a list object? For example, say my workspace is as follows ls() [1] "x" "y" "z" and suppose I want to put these objects inside a list object, say object.list <- list() without having to explicitly write down their names as in object.list$x = x object.list$y = y object.list$z = z Is

Several bugs are present in R-2.15.3 and R-alpha due to naive copying of list elements. The bug below is due to naive copying in subset.c (with similar bugs for matrices and arrays): a<-list(c(1,2),c(3,4),c(5,6)) b<-a[2:3] a[[2]][2]<-9 print(b[[1]][2]) Naive copying in mapply.c leads to the following bug: X<-1+1 f<-function(a,b) X A<-mapply(f,c(1,2,3),c(4,5,6),SIMPLIFY=FALSE)

I am running R 2.0.0, GOstats 1.1.1 and GO 1.7.0, and when I use the function GOHyperG, I have the following error: w1<-as.list(hgu95av2LOCUSID) w2<-unique(unlist(w1)) set.seed(123) myLL<-sample(w2,100) xx <- GOHyperG(myLL) Error in mget(x, env = GOTERM, ifnotfound = NA) : recursive default argument reference In fact first I tried this function with my locusId ' list (with

Hi, I have a list of IPI gene IDs. I want to find out whether there is a package which can map the gene ontology to these IPIs, and plot the pie chart to demonstrate the molecular function distributions. The input is like the following gene IPI IDs: IPI:IPI00008860.1|SWISS-PROT:Q9BXJ4-1|TREMBL:Q542Y2|ENSEMBL:ENSP00000231338;EN

In my R learning I've come across a situation in which a piece of code that works on the work space outside a function does not work inside the function. WARNING THIS EMAIL CONTAINES THE CODE:#rm(list=ls()) THIS WILL CLEAR ALL OBJECTS FROM YOUR WORKSPACE! When I use rm(list=ls()) and then ls() it shows character(0) So I tried to make a quick function to speed this up as follows:

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

Hi, I have a set of matrices (MAT.1, MAT.2, ...) and I'd like to perform the same operation on each of them (for simplicity, say . I'm writing a function for this so that it can be repeated for different sets with different numbers of matrices. The matrices have the same number of columns, but do not have the same number of rows. My thought is to loop thru the set. but I'm not sure

Hi I want to simplify my problem into a prototype, how to write a function to get all the object in your current environment, e.g. .GlobalEnv, and print their mode? For example, if I have object a,b,c... in my environment, a=1;b='test';c=matrix(0,3,3)..... I want to write a function myfun(), when I run myfun(), this retrieve all the objects in my environment automatically and print

Hi folks, I need to search the dataset on data with name on heading; Run conc density I look at ??help.search and could not resolve; help.search(pattern, fields = c("alias", "concept", "title") What shall I replace "pattern"? I suppose replacing "alias", "concept", "title" with "Run", "conc",

Hello, How ls() only functions or only data objects (basically anything other than functions) such as data.frame, numeric ...? John [[alternative HTML version deleted]]

Dear All, It seems that reference classes consume a lot of memory which became a problem for my rather extensive simulation. I prepared a small example. An instance of this minimal class uses about 20K on disk. rm(list=ls(all=TRUE)); MySmallClass = setRefClass("MySmallClass", fields = list( myField = "numeric" ), methods = list( initialize =

Hi, I am new to R and have a couple of questions. I know how to list all objects (with ls()), but how to list all properties of them? For instance, I found function object.size(), but I would also like to know whether one object is a dataset or just one vector (variable) or even only one value, etc... And another question - how to save workspace to a custom location while running R? Is there

Dear R Helpers, A few weeks ago I asked for some help on how to accomplish modifications to data in a set of data frames. As part of that request I mentioned that I realized that one way to accomplish my goal was to put the data frames together in a list but that I was looking for a way to do it with data frames and a loop because I "believe the better thing is to work df by df for my

I think the discussion of this issue has gotten more complicated than necessary. First, there really is a bug. You can see this also by the fact that delayed warning messages are wrong. For instance, in R-3.1.2: > lapply(c(-1,2,-1),sqrt) [[1]] [1] NaN [[2]] [1] 1.414214 [[3]] [1] NaN Warning messages: 1: In FUN(c(-1, 2, -1)[[3L]], ...) : NaNs produced 2: In

On 04.06.2017 11:50, jing hua zhao wrote: > Hi All, > > > I wonder if there should be one character for quote= in read.table, i.e., > > >> args(read.table) > function (file, header = FALSE, sep = "", quote = "\"'", dec = ".", > ... > > I have a file containing the following lines, > > > 08248-GOTERM

Hi, There are quiet a few different 'apply' functions, such as lapply, sapply and many more. I'm very familiar with the 'Apply' function in Mathematica. Can somebody point me a summary of all the 'apply' functions in R. Also, I'm curious that what 'l' and 's' (and other prefixes) stand for in 'lapply' and 'sapply' Regards, Peng