similar to: How to import the large data into R

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other

Hi Mr Tierney, I have noticed an error message from R 1.12.x's CMD check for a while (apparently prof Ripley completely rewrote CMD check in R 1.12+) e.g.: http://bioconductor.org/checkResults/2.7/bioc-LATEST/snpMatrix/lamb2-checksrc.html ---------------- * checking R code for possible problems ... NOTE Warning: non-unique value when setting 'row.names': ?new? Error in

Dear R experts I was using kinship package to fit mixed model with kinship matrix. The package looks like lme4, but I could find a way to extract p-value out of it. I need to extract is as I need to analyse large number of variables (> 10000). Please help me: require(kinship) Generating random example data id <- 1:100 dadid <- c(rep(0, 5), rep(1, 5), rep(3, 5), rep(5, 5), rep(7,

Dear R-Helpers, I am using qtl package to analyze qtl data from QTL cartographer. I have the map file and cro file from QTL cartographer. I was trying to import these two files in R using qtl package. data=read.cross("qtlcart", ".", "crofile.txt", "mapfile.txt") ### I have matched the file structure with the one on the website of qtl package - It matches

Hi R-help folks, I have been doing some single SNP association work using snpMatrix. This works well, but produces a lot of false positives, because of population structure in my data. I would like to correct the p-values (which snpMatrix gives me) for population structure, possibly using principle component analysis (PCA). My data is complicated, so here's a simple example of what

I have had some fun in the last few days trying to put together an annotated map of China with R and some public GIS data: http://sourceforge.net/projects/outmodedbonsai/files/snpMatrix%20next/1.17.7.11/China_Choropleth_Maps.pdf/download It is done, and rather nice... there are a few issues: - the default pdf() device cannot do CJK with embedded fonts - and cairo_pdf() is not hooked up to

Hi I used the command R CMD INSTALL ncdf to install ncdf package in linux. Can somebody explain to me what might be wrong. Thanks. Below is the error. * Installing *source* package 'ncdf' ... Special note: checking for gcc... gcc checking for C compiler default output... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for

Having trouble with netCDF since I upgraded to 1.2.1 (did directly from 1.1.1). Package was recompiled after the upgrade. Symptoms: open.netCDF returns cleanly, but read.netCDF causes R to segfault and dump core. What else do you need me to write to help? --please do not edit the information below-- Version: platform = i586-pc-linux-gnu arch = i586 os = linux-gnu system = i586, linux-gnu

Hello, I have a large data set 320.000 rows and 1000 columns. All the data has the values 0,1,2. I wrote a script to remove all the rows with more than 46 missing values. This works perfect on a smaller dataset. But the problem arises when I try to run it on the larger data set I get an error “cannot allocate vector size 1240 kb”. I’ve searched through previous posts and found out that it might

Greetings. I am attempting to add NetCDF libraries within R, and have failed. We have R version 2.8, and are running on a 64-bit Redhat Linux 2.6.18 kernel: Red Hat Enterprise Linux Client release 5.2 (Tikanga) Linux halfmoon.ncdc.noaa.gov 2.6.18-92.1.22.el5 #1 SMP Fri Dec 5 09:28:22 EST 2008 x86_64 x86_64 x86_64 GNU/Linux I have run the installation instructions found at

I have a 2 x 3 matrix called snp and I want to compute the following probability: choose(sum(snp[,1]), snp[1,1]) * choose(sum(snp[,2]), snp[1,2]) * choose(sum(snp[,3]), snp[1,3])/choose(sum(snp), sum(snp[1,])) but I keep getting Infs and NaNs. Is there a function that can do this in R? -- Thanks, Jim. [[alternative HTML version deleted]]

summary: I can successfully ncvar_put(...) data to a file, but when I try to ncvar_get(...) the same data, I get > Error in if (nc$var[[li]]$hasAddOffset) addOffset = nc$var[[li]]$addOffset else addOffset = 0 : > argument is of length zero How to fix or debug? details: R code @ https://github.com/TomRoche/GEIA_to_NetCDF successfully (if crudely) uses R packages={ncdf4, maps, fields}

Hi, I am new to R. and even though I've made my code to run and do what it needs to . It is taking forever and I can't use it like this. I was wondering if you could help me find ways to fix the code to run faster. Here are my codes.. the data set is a bunch of 0s and 1s in a data.frame. What I am doing is this. I pick a column and make up a new column Y with values associated with that

Hi, I cant understand where I am going wrong.Below is my code.I would really appreciate your help. Thanks. > genfile<-read.table("c:/tina/phd/bs871/hw/genfile.txt",skip=1) > > #read in SNP data > snp.dat <- as.matrix(genfile) > snp.name <- scan("c:/tina/phd/bs871/hw/genfile.txt",nline=1,what="character") Read 100 items

I am looking for a package to read and write NetCDF files. NetCDF package says it can only read, not write. Another package for the standard binary file format? Daehyok Shin

Dear R experts, I have 2 matix: A& B. I am trying to index B against A - (1) find out B rows that fall between the col 1 and 2 of A& put them into a new vector SNP.I made code as below, but I cannot think of a right way to do it. Could anyone help me with the code? Thanks,Jiang---- A <-

Dear R colleagues, I annotated a list of single nuclotide polymorphiosms (SNP) with the corresponding genes using biomaRt. The result is the following data.frame (pasted from R): snp ensembl_gene_id 1 rs8032583 2 rs1071600 ENSG00000101605 3 rs13406898 ENSG00000167165 4 rs7030479

Hi I listened to all your advise and ran my data on a computer with a 64 bits procesor but i still get the same error saying "it cannot allocate a vector of that size 1240 kb" . I don't want to cut my data in smaller pieces because we are looking at interaction. So are there any other options for me to try out or should i wait for the development of more advanced computers!

Hi, I'm trying to melt() some data for subsequent cast()ing and am encoutering errors. The overall process requires a couple of casts()s and melt()s. ########Start Session 1########## ## I have the data in a (fully) melted format and can cast it fine... > norm1[1:10,] Pool SNP Sample.Name variable value 1 1 rs1045485 CA0092 Height.1 0.003488853 2 1 rs1045485

Hi, Following my earlier posts about having problems performing a PCA, I have worked out what the problem is. The problem lies within the PLINK to gds conversion. It seems as though the SNPs are imported as "samples" and in turn, the samples are recognised as SNPs: >snpsgdsSummary("chr2L") Some values of snp.position are invalid (should be > 0)! Some values of