similar to: Needing a better solution to a lookup problem.

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

Hi all, We are using two methods to identify SNPs. One is based on resequencing the genome and aligning the reads to the sequenced genome to identify SNPs (data available for 44 individuals). Another is based on SNP array with selected loci (30000 loci, 870 individuals). I want to compare the results from the resequencing based minor allele frequency and Array based minor allele frequency.

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 =

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

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

Hello all, I am trying to make a genome association plot for p-values related to SNPs and was fortunate to find that R contains a package that produces Manhattan plots which is what's preferred for my current project. The function mhtplot() is found in the 'gap' package which I installed in R 2.11.1 on Windows. I thought I'd test out the function first with the examples they

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 everyone, I have a data frame Gene with SNPs eg. P1 P2 P3 CG CG GG -- -- AC -- AC CC AC -- AC I tried to replace all the GG with a value 3. Gene[Gene=="GG"]<-3 It always give me: Warning in `[<-.factor`(`*tmp*`, thisvar, value = 3) : invalid factor level, NAs generated Does any know if there is anything wrong with my code? Thanks, Zhengyu

i have two RData files,,i want to print them to check the format of the tables in these files,,,i can load both the files and can read it as well > load('ann.RData') > str(ann) List of 4 $ Name : chr [1:561466] "rs3094315" "rs12562034" "rs3934834" "rs9442372" ... $ Position : int [1:561466] 742429 758311 995669 1008567 1011278 1011521

Hello, I would like to plot specific SNPs with their exact locations on a chromosome. Based on my genotyping results I would like to separate these SNPs in three different categories: 1, 2 and 3 and use different colours to represent these categories. The script below generates the sample data. I can plot these with the image function using the following: val <- 1:3 samp <- sample(val,

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

Hello, I have an R script that I use as a template to perform a task for multiple files (in this case, multiple chromosomes). What I would like to do is to utilize a simple loop to parse through each chromosome number so that I don't have to type the same code over and over again in the R console. I've tried using: for(i in 1:22){ etc.. } and replacing each chromosome number with

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 - MI0005821 106 gen3 2L 159838 159928 + MI0005813 90 gen7 2L

Thanks. I think nabble is good for programming questions. Bear with me if I'm incorrect. Data: Genomics SNP information Goal: I need to add Chromosome and SNP position to the data frame I'm using through apply. I'd like to add new column from text processed through apply function. For example: 10:60523:T:G (Column 2) CHR: 10 Position: 60523 Dataset: chr rs ps n_miss allele1

Hi,     I want to use segChrom() method in tilingArray package. For that I need to create a probeAnno object. I could not find much much info by ?probeAnno. I need help in creating  probeAnno object. Snap shot of the file(.txt): chr1 2500014 2500038 + 0.232689943122845 chr1 2500039 2500063 + 2.60502410304227 chr1 2500062 2500086 + 0.0756595313279895 chr1 2500080 2500104 + 0.78574617788405 chr1

Dear all. I need to draw a scatter plot of 23 chromosome copy numbers (y axes) against chromosome and physical location within each chromosome in one plot. The data matrix looks as below: chr location copy_num 1 118345 1.320118 1 3776202 1.133879 1 4798845 0.989997 1 5350951 1.100967 . more data here . . 2 118345 2.459119 2 157739 1.915919 2 1530065 1.924372 2

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

Hi R-ers, I am struggling with my x-axis in a association plot. What I would like is to place the labels of the x-axis between the tick markers and normally the labels are printed at the place where the tick marker is placed. I don???t want to move the tick marker (it gives the switch between one chromosome and the next) but I just want to put the chromosome number in between the

Hello, I'm (eventually) attempting a singular value decomposition of a 3200 x 527829 matrix in R version 2.10.1. The script is as follows: ###---------Begin Script here-------### library(Matrix) snps <- 527829 ## Number of SNPs N <- 3200 ## Sample size y <- rnorm(N, 100,1) ## simulated phenotype system.time( ## read in matrix

I have a dataframe in the general format: chr1 0.5 chr1 0 chr1 0.75 chr2 0 chr2 0 chr3 1 chr3 1 chr3 0.5 chr7 0.75 chr9 1 chr9 1 chr22 0.5 chr22 0.5 where the first column is the chromosome location and the second column is some value. What I'd like to do is have a histogram created for each chr location (i.e. a separate histogram for chr1, chr2, chr3, chr7, chr9, and chr22). I am just