similar to: Multiple testing and Logistic regression in case control studies

Dear R-nautes, I installed the 2.7.1 version of R and found it is not possible to modify graphical parameters with par(). for example; > par(mfrow=c(2,2)) Error in c(2, 2) : unused argument(s) (2) > par$mfrow NULL Does any one know what is the cause of this problem? Regards, Fabio -- Fabio Sánchez, MD, MSc, PhD Unit of Dermatology and Venereology Department of Medicine Karolinska

Dear R community, I am not experienced in writing functions and need your help to understand the strategy to face the following problem: I have a group of independent numerical variables, let's say a<-c(1,3,2,6,9,2,2,3,4,1) b<-c(2,3,3,4,5,6,2,1,1,6) c<-c(0,2,4,4,7,6,7,1,2,2) d<-c(0,0,0,1,0,2,1,3,1,2) e<-c(9,2,3,1,1,1,0,2,5,6) and a grouping variable,

Hi, I would like to get guidance as to how to write code in R that can deal with the following situation: v1 is a vector containing a sequence of numbers (Ex. 1:10) I want to store the sequence of numbers resulting from multiplying the first and the second element in the vector, then the product of the 1st, 2nd and 3rd, then 1st,2nd,3rd and 4th and so forth until all the elements in the

Dear all,   I have data from the following experimental design and trying to fit a mixed model with lme function according to following steps but struggling. Any help is deeply appreciated.   1) Experimental design: I have 40 plants each of which has 4 clones. Each clone planted to one of 4 blocks. Phenotypes were collected from each clone for 3 consecutive years. I have genotypes of plants. I

Dear all, I am running qtl mapping. I have 75 RI lines with some residual heterogeneous loci. The loci are code A, B or H(heterogeneous). Questions: 1) R/qtl determine the data is F2 intercross. 2) Warning message about strange genotype pattern > library(qtl) > dat=read.cross("csv", file="rqtl_trt.csv") --Read the following data: 75 individuals

Dear experts, I am trying to perform an association using snpStats. I have a snp matrix called 'plink' which contains my genotype data (as a list of $genotypes, $map, $fam), and a phenotype data frame which contains the outcomes (outcome1, outcome2,...) I would like to associate with the genotype. My question is, how do I loop through the outcomes? This type of data seems different from

I partly answered my question since independence_test() function in coin package apparently do Cochran-Armitage trend test just like Eric Lecoutre's function tabletrend() - slightly modified here: > independence_test(pheno ~ geno, data = dat2, teststat = "quad", scores = list(geno = c(0, 1, 2))) Asymptotic General Independence Test data: pheno by groups 1 < 2

In case there are users of the TeX macro package ConTeXt on this list, they may be interested to know that it is now possible to include R code in a ConTeXt document and have the code evaluated while compiling. The inverse of Sweave, as it were. The advantage is that there is then only one file to keep track of (.tex vs .rnw and .tex), while a drawback is speed, since each code snippet is

Dear all, we seek a talented and motivated post-doc to develop computational methods for inferring the molecular basis of genetic diseases by integration of personal omics data. Research topics include: identifying causal mutations of rare disease patients by meta-analysis; inferring disease-causing molecular pathways from genotype, phenotypes, and omics profile of patient-derived cell lines

I'm working in a Gen/Marker-Phenotype association study in wheat and I'm using a Mixed Model Approach to estimate the effect of the markers. My model has the atribute measured as y (response variable), the markers and the blocks (of a complete random block design) as fixed and the genotypes and the residuals as random. In one hand I'm assuming that there is no correlation between

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 a plot similar to the following library(lattice) stripplot(1:15, rep(1:3, each=5)) In order to save space for a presentation, I would like to have horizontal strips instead of vertical. The argument 'horiz' turns the arguments around, but not the plot. The documentation for 'stripplot' ('xyplot'), 'panel.stripplot' and the FAQ do not seem to provide

Hi, I am conducting an association analysis of genotype and a phenotype such as cholesterol level as an outcome and the genotype as a regressor using multiple linear regression. There are 3 possibilities for the genotype AA, AG, GG. There are 5 people with the AA genotype, 100 with the AG genotype and 900 with the GG genotype. I coded GG genotype as 1, AG as 2 and AA as 3 and the p-value for the

*Bioinformatics Specialist, Sage Bionetworks, Seattle, WA* Sage Bionetworks is a world-leading nonprofit biomedical research organization dedicated to: (1) developing predictive models of disease-related phenotypes through integrative analysis of large-scale genomic data sets; (2) building and supporting an open source compute platform and database to more effectively harness genome-scale data by

Hi, I am trying to test for pairwise associations between genotypes ( Rows=individuals, Columns =genes, data are up to 4 genotypes per gene, some with 2,3 or 4) where each chisquare comparison is different depending on the genes tested. The test is the observed multilocus (across columns for each individual) genotypes vs the expectation, which is the product of the individual frequency for each

Dear R-experts, My problem is how to handle a 10GB data file containing genotype data. The file is in a particular format (Illumina final report) and needs to be altered and merged with phenotype data for further analysis. PERL seems to be an frequently used solution for this type of work, however I am inclined to think it should be doable with R. How do I open a text-file, line by line,

Dear list! I have run into a problem that seems very simple but I can't find any solution to it (have searched the internet, help-files and "An introduction to R" etc without any luck). The problem is the following: I would like to create a data.frame with two components (columns), the first component being a matrix and the second component a vector. Whatever I have tried so far, I

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 <-

Dear Sir/Madam, Since a few day now I try to use the command "polygenic" from the GenAbel package. However, I keep bumping up against an error message: "Error in polygenic(Testo, kin = kinship, data = data1) : dimension of outcome and kinship.matrix do not match". My data exists of 1240 individuals with 74 markers. It mainly consists of small families (2 or more brothers,

I am receiving the above error ( full r session output below) the script runs OK in windows. and "genotypes" and "ploidy" are both correct arguments any suggestions would be most welcome Nevil Amos MERG/ACB Monash University School of Biological Sciences > library(Geneland) Loading required package: RandomFields Loading required package: fields Loading required