similar to: problems when loading package GenABEL

Hi all, I am just beginning to use R and encountered a problem in trying to draw a regression line using the command "abline(coef(var)" and similar ones but got the error "plot.new has not been called yet". Does anybody know how can I call plot.new? Is this an additional package to be found somewhere on the web? Is it a functionality that I just have to "activate"

Hi all, I am already using R under Window and would like now to try and install it under Unix; I read I need tcl/tk installed so I connected to http://www.scriptics.com downloaded the file and extracted them to a directory tcltk beside R. I configured (./configure) both packages (tcl and tk) and compiled (make) them but I am not sure about how to proceed now: should I launch the command make

Good evening, I am trying to add labels to the point of a simple plot, using the text() function; the problem is that sometimes, if two points are too close to each other, labels overlap and are no longer readable. I was wondering whether there are options that I can use to prevent this overlapping (by, for example, placing labels alternatively above and below the plotted curve), or whether I

Good morning, I am trying to recode the values of a column in a data frame and, instead of using a long series of if/else statements I would like to use a switch (as it is, for instance, in the C programming language). I have a column of this type: AT BB B1 B1 CC CC T6 B1 CC BB TT AT AT AT TT BB ... and I need to change this coding (if it's AT then it should be A1, if it's BB then

Hello, I have a list with n numerical components of different length (3, 4 or 5 values in each component of the list); I need to export this as a text file where each component of the list will be a row and where missing values should fill in the blanks due to the different lengths of the components of the list. I think that as a first step I should convert my list to a data frame, but this is

Hi all, I would like to know which are the main differences between R under Windos and R under Linux/Unix and where I can find, if something exists, some materials and infos on line on this topic. Thank you very much, Filippo Biscarini *************************** Filippo Biscarini, Research and Development ANAFI (Italian Holstein Association) Via Bergamo, 292 26100, Cremona, Italy

Good morning, I am merging two datasets and I would like to save the non-matching rows in a separate file. The problem is how to retrieve the non-matching rows in R. Example: DATASET A code nomi A1 Franco A2 Mario A3 Andrea A4 Sandro A5 Luca DATASET B code book A1 Guerra e Pace A1 Storia di Roma A2 La coscienza di Zeno A4

Hi all! I am using GenABEL on R for GWAS analysis. I am having a couple of issues: First, I am having a problem reading files (.map, & .ped, size 900Mb, using windows 32-bit) onto R in the "convert.snp.ped" statement. I am thinking this problem is likely due to the large size of the files & my version of R is not able to handle them, since I can read in smaller files.

Does anyone use the R library GenABEL? I am using it to calculate SNP interactions. I have a list of 100 SNPs, I need to look at the interaction between each of two SNPs among the list. my question is how to perform this in GenABEL. I want to use the "lm" function, but don't know how to use the SNP information. for example: result <- (lm(y~SNP1+SNP2+SNP1*SNP2)) the problem here

Hi all! I am trying to install package - GenABEL in a Linux (RedHat) environment using R 2.6.2. The CRAN Mirror starts up, I select the site, but I end up with the following error: ****************************************************************** Warning: unable to access index for repository http://cran.stat.ucla.edu/src/contrib Warning messages: 1: In open.connection(con, "r") :

Hi, I'm using kinship2 to calculate heritabilty, but I would like calculate in GenABEL too. I trying the code: > require(kinship2) > require(GenABEL) > pedig = with(Dados, pedigree(id=IID, dadid=PAT, momid=MAT, sex=SEX, famid=FID, missid=0)) > kmat = kinship(pedig) > (mod1 = polygenic(altura ~ SEX + idade, data=Dados, kin=kmat)) Erro em intI(i, n = d[1],

Hi, I've been trying to use the impute2mach function in the GenABEL library. I unfortunately cannot make a working example as when I scale down the files I no longer get an error message. The error message that I get on the full file is: Error in checkSlotAssignment(object, name, value) : assignment of an object of class "NULL" is not valid for slot "data" in an

Hi, I had originally posted regarding an error when trying to install package - GenABEL - it has now become clear that R is not able to connect to the net. Below are a couple of things I've tried with the resulting errors I am running R 2.6.2 on Linux e15 X86 How can I fix this? Thank you! 1) download.file("http://www.nytimes.com", destfile<-tempfile()) Error: trying URL

Hi all! I am desperately trying to figure out the solution to this error, but nothing as of yet is working. As noted in an earlier post I am using GenABEL. In an attempt to read in the phenotype file, in the format .dat, R keeps giving me the error "more columns than column names" I have tried to read in the data without the headers; I have also tried to trim the data to remove any

Hi, I'm a new contributor. I'm considering the possibility of adopting a third-party JSON library instead of LLVM's homegrown `lib/Support/JSON.cpp`. The way I see it, this would bring several advantages as well as some downsides: + Slimmer codebase. + Benefit from upstream work and active contributions to another project. + Possibly improved performance and API ergonomics. -

Hi, when I try to compile an llvm program, it gives me the following error. Do you have idea on what I should look for? Thanks, Filippo llvm-as -f -o arith.bc arith.bc.exp llvm-as: Type.cpp:1034: void llvm::DerivedType::notifyUsesThatTypeBecameConcrete(): Assertion `AbstractTypeUsers.size() < OldSize-- && "AbstractTypeUser did not remove itself from the use list!"'

Hi all, I have a basic plot MC_P1.DEM.1<-qplot(x=Group, y=P1.DEM.UN.WPP.FER.TOT_var, data=GroupMeans_gr_DEM, geom="bar", stat="identity", fill=Group)+ myScale_fill()+getLabs("MC_P1.DEM.1") I would like to add a y-lab horizontally ON TOP OF y-axis...and I didn't understand how it works (with axis.text.y???how) thanks a lot filippo [[alternative HTML

[please CC me on replies, I'm not subscribed] Hi, I'm trying to get dmraid 1.0.0rc9 [0] to compile with --enable-klibc, however I have some troubles with mkfifo defined in /usr/lib/klibc/include/sys/stat.h. /usr/lib/klibc/include/sys/stat.h: In function 'mkfifo': /usr/lib/klibc/include/sys/stat.h:28: error: 'S_IFMT' undeclared (first use in this function) after

Package: logcheck Version: 1.3.5 Severity: minor Hi, reading logcheck source it seems that it requires nail for MAILATTACH to work, however it is not suggested/recommended. (JFTR it is debatable if nail is appropriate or something else should be used) thanks, filippo -- System Information: Debian Release: squeeze/sid APT prefers unstable APT policy: (990, 'unstable'), (500,

Package: logcheck-database Version: 1.3.5 Severity: normal Hi, I was having a look at logcheck and why I received a "verification failed: Temporary failure in name resolution" as a _system_ message. Turns out that since violations.d/logcheck is empty now, most of the rules in violations.ignore.d look quite useless, can you confirm? I suspect that a big part of those rules should be