similar to: New version of the LDheatmap package

Dear R-helpers, I am developing a package named LDehatmap. It depends on the "genetics" package and includes two data files and a demo file. When I'm trying to install it, I get the following messages: * Installing *source* package 'LDheatmap' ... ** R ** data ** demo ** help >>> Building/Updating help pages for package 'LDheatmap' Formats: text html

Is there any way to store the value of warnings but avoid printing them? A simplified example: > out <- c(0.2,0.3,0.4) > var <- c(2,3,4) > outcome <- glm(out ~ var, family=binomial()) Warning message: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) I don't like the warning printed, but I would like to be able to check it's value after the

Hi, I'm new to calling C++/C programs from R and am having some trouble getting started. Following Sigal Blay (Simon Fraser University)'s instructions, I have a .c file called "useC1.c": /* useC1.c */ void useC(int *i) { i[0] = 11; } This produces a .o file : "useC1.o" in a specified directory. I then open R, set the proper directory and:

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, 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

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

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

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

Dear All, I would like to ask for help on how to read different files automatically and do analysis using scripts. 1. Description of the data 1.1. there are 5 text files, each of which contains cleaned data for the same 100 SNPs. Observations (e.g., position on gnome, alelle type, ...) for SNPs are rows ordered by the SNP numbers, 1.2. there are 1 text file, containing the expression level of

This will probably seem very simple to experienced R programmers: I am doing a snp association analysis and am at the model-fitting stage. I am using the Stats package's "drop1" with the following code: ##geno is the dataset ## the dependent variable (casectrln) is dichotomous and coded 0,1 ## rs743572_2 is one of the snps (which is coded 0,1,2 for the 3 genotypes)

Need way to resize an existing graphics window. This should be applicable across platforms (as part of a package). Context: function1() draws main plot (I'm using grid), function2() adds smaller plot above main plot, but this one can sometimes overflow the original graphics window area. Thanks, Sigal

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

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

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.

Hello, I have a data frame like this: > head(SNP) mean var sd FQC.10090295 0.0327 0.002678 0.0517 FQC.10119363 0.0220 0.000978 0.0313 FQC.10132112 0.0275 0.002088 0.0457 FQC.10201128 0.0169 0.000289 0.0170 FQC.10208432 0.0443 0.004081 0.0639 FQC.10218466 0.0116 0.000131 0.0115 ... and I am creating plot like this: s <- ggplot(SNP, mapping = aes(x = mean, y = var))

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 all, need help very urgently I did stepwise logistic regression for 35 covariates and added one SNP out of (500000) to get the best model for each model As my professor asked me using this command, outfiles <- paste(colnames(snps), ".txt", sep="") # list of output files for the best models for(i in 1:ncol(snps)) { model <- glm (Pheno~var1+var2+var3+..(all

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

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

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