similar to: Working with massive matrices in R

Hi, The program below work very well. (snps = c('rs621782_G', 'rs8087639_G', 'rs8094221_T', 'rs7227515_A', 'rs537202_C')) Selec = todos[ , colnames(todos) %in% snps] head(Selec) But, I have a data set with 1.000 columns and I need extract 70 to use (like snps in command above). This 70 snps are in a file. So I create a file to extract them with

I have a solution (actually a few) to this problem, but none are computationally efficient enough to be useful. I'm hoping someone can enlighten me to a better solution. I have data frame of chromosome/position pairs (along with other data for the location). For each pair I need to determine if it is with in a given data frame of ranges. I need to keep only the pairs that are within any of

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

Dear R-devel, I am writing for help on how I should include parallel sets of data in my package. Brief summary: I am new to using data within packages. I want a user to be able to specify one of two alternative versions of within-package datasets to use, and I want to load just that one. I have a solution that works, but it doesn't seem as simple as it should be from a user's

If I run an analysis which generates statistical tests on many SNPs I would naturally want to get more details on the most significant SNPs. Directly from within R one can get the information by loading RSNPer (from Bioconductor) and simply issuing a command SNPinfo(2073285). Unfortunately, the command cannot handle a vector and therefore only wants to do one at a time. I tried the lapply and

Dear all, After struggling for some time with *apply() and eva() without success, I decided to ask for help. I have 3 lists labeled with, each contains 3 different interpolation functions with identical names: > names(missgp0) [1] "spl.1mb" "spl.2mb" "spl.5mb" > > names(missgp1) [1] "spl.1mb" "spl.2mb" "spl.5mb" > >

Dear R developers: I am a PHD candidate student in the school of public health of Peking University and my major is genetic epidemiology. I am learning the FAM-MDR algorithm, which is used to detect the gene-gene and gene-environment interactions in the data of pedigree. The codes were written by Tom Cattaert of the University of Liege. The algorithms and the sample datasets are available at

I a using plink on a large SNP dataset with a .map and .ped file. I want to get some sort of file say a list of all the SNPs that plink is saying that I have. ANyideas on how to do this? -- Thanks, Jim. [[alternative HTML version deleted]]

Hi All, I have a problem with weighted logistic regression. I have a number of SNPs and a case/control scenario, but not all genotypes are as "guaranteed" as others, so I am using weights to downsample the importance of individuals whose genotype has been heavily "inferred". My data is quite big, but with a dummy example: > status <- c(1,1,1,0,0) > SNPs <-

snpMatrix package is quite nice (read.plink())

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

Hello, I did a pca with over 200000 snps for 340 observations (ids). If I plot the eigenvectors (called rotation in prcomp) 2,3 and 4 (e.g. plot (rotation[,2]) I see a strange "column" in my data (see attachment). I suggest it is an artefact (but of what?). Suggestion: I used prcomp this way: prcomp (mat), where mat is a matrix with the column means already substracted followed by a

Hi, Does anybody know how to obtain the imputed SNP genotype probabilities from the snpStats package? I am interested in using an imputation method implemented in R to be further used in a simulation study context. I have found the snpStats package that seems to contain suitable functions to do so. As far as I could find out from the package vignette examples and its help, it gives the

Dear Mme/Mr. Hope you are doing well. I am doing some genetic analysis using The R software and I have difficulties to find how I can perform an Interaction/epistasis analysis using 3 or more SNPs (=markers) ? (In the instructive manual, there is only an interaction/epistasis analysis with 2 markers). In addition can you please inform me how I can perform Haplotype analysis and if there is an

Hi, I am using the sim1000G R package to simulate data for case/control study. I can not figure out how to manipulate this code to be able to generate 10% or 50% causal SNPs in R. This is whole code provided as example on GitHub: library(sim1000G) vcf_file = "region-chr4-357-ANK2.vcf.gz" #nvariants = 442, ss=1000 vcf = readVCF( vcf_file, maxNumberOfVariants = 442 ,min_maf =

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

I'm pretty new to R, and I've been given a script by a user who wants some help with it. I know enough about the way R works to know that this is a very inefficient way to do what the user wants (the LSB_JOBINDEX stuff is added by me so that this can work on many hundreds of input data files as LSF jobs - it's the nested loops I'm really interested in):

Hello, I have indicators for the present of absent of a snps in columns and the categorey (case control column). I would like to extract ONLY the tables and the indices (SNPS) that give me 2 x 3 tables. Some gives 2x 2 tables when one of the allelle is missing. The data look like the matrix snpmat below: so the first snp should give me the following table: (aa=0, Aa=1 and AA=2) aa

Dear useRs, First off, sorry about the long post. Figured it's better to give context to get good answers (I hope!). Some time ago I wrote an R function that will get all pairwise interactions of variables in a data frame. This worked fine at the time, but now a colleague would like me to do this with a much larger dataset. They don't know how many variables they are going to have in the

Dear All, Does anybody have experience with R package pbatR (http://cran.r-project.org/web/packages/pbatR/index.html)? I am trying to use it to analyze the family-based case-control data, but the package totally doesn?t work on my computer. I contacted the authors of the package, but I haven?t heard anything from them. Following the package manual, I tried the simple example as below: