search for: phenotypic

Hello all, I'm having difficulty with setting up a mixed model using lme in the nlme package. To summarize my study, I am testing for effects of ornamentation on foraging behavior of wolf spiders. I tested spiders at two different ages (penultimate vs. mature) and of two different phenotypes (one species tested lacks ornamentation throughout life [non-ornamented males] while the other

Dear R users, Could you help my with the following problem? I want to repeat a glm analysis with 2 independent variables for all 900 variables (snps) in my data set. So, I want to check whether snp1 has a different effect on my outcome variable in patients and controls(phenotype). And repeat that for snp2 to snp900. Is there an easy way to get a summary of the data, e.g. a list of P values of all

Hey, I have code that can check the quality of a data set we're working with (expression data), and I'm having some trouble writing code that would make the expression data we have tie to other data we want to link it to (called phenotype data). Does anyone have any advice on how I could make a single object that would do this? Other relevant info: I want to use the pdata() function,

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 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

I have a path: path = "/nfs/users/nfs_n/ns9/ Phenotype Analysis/Results/Run_AmplRatio_neg BinaryAll trained without akapn+tnik.csv" I wish to replace the spaces with "\ " so that it can be read by a system call to unix. Using gsub I try: > gsub(" ","\\ ",path) [1] "/nfs/users/nfs_n/ns9/Phenotype Analysis/Results/Run_AmplRatio_neg BinaryAll

Hoping someone can offer me some assistance. I'm trying to execute a script and I keep getting this error message about "Error: element 12 is empty". I'm wondering if my syntax is incorrect within legend.list. If anyone has any suggestions to sees something obvious that I am missing, I would greatly appreciate any help. Many Thanks, Patrick > # These are the symbols and

...t; = missing data. "Phenotype" = a continuous variable of interest. I have a much larger number of columns corresponding to genes (i.e., more columns with the "SNP_" prefix) in my real dataset. For each gene in turn (i.e., each "SNP_" column), I would like to find the phenotypic variance for all of the plants with non-missing data. Note that the plants with missing genotype data ("NA") differ for each gene (each "SNP_" column). Would one of you be able to offer some specific code that could do this operation? Please rest assured that I am not a student...

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

...0000 0.00 0.3333333 b 0.0000000 1.00 0.0000000 0.25 0.0000000 c 0.5000000 0.00 1.0000000 0.00 0.1666667 d 0.0000000 0.25 0.0000000 1.00 0.0000000 e 0.3333333 0.00 0.1666667 0.00 1.0000000 basically these two matrices are the similarity matrices between the patients. x1 is genotypically and y1 is phenotypically. Now I want to generate a plot to see which patients have high similarity genotypically as well as phenotypically. So I am using plot(x1[upper.tri(x1)],y1[upper.tri(y1)]) #taking only the upper triangle of matrices as other half is same. The plot is coming fine.But I am loosi...

Hi, I'm looking for an efficient code that will enable me to reshuffle data (phenotype) for certain number of individuals and creating a loop that will randomly simulate it for 10000 times *(permutation)*. I also need to find how I keep the information (p value for each SNP) gathered for all the 10000 iterations. My data set looks like this (n=500): Individual # Phenotype SNP1 SNP2

Hi, My query is regarding permutation test and reshuffling of genotype/phenotype data I have been using the haplo.stats package of R. for haplotype analysis and I would like to perform an analysis which I'm requesting your advice. I have a data set of individuals genotyped for 12 SNP and a dichotomous phenotype. At first, I have tested each of those SNP independently in order to bypass

Hello, I have data in a dataframe with 139104 rows which is multiple of 96x1449. i have a phenotype file which contains the phenotype information for the 96 samples. the snp name is repeated 1449X96 samples. I haveto merge the two dataframes based on sid and sen. this is how my two dataframes look like dat<-data.frame(snpname=rep(letters[1:12],12),sid=rep(1:12,each=12),

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

Hi: I use lm (linear model) to analyze 47 variables , 8 responses So I use loop to finish it . I want the program to show the results that P-value is less than 0.05. How can I cite the P-valus from lm result ? Ping The code: #using LM to model general fati for (j in 48:52) { for (i in 3:46){ gen.fat<-y_x[,j] gen.fat<-as.numeric(gen.fat) snp_marker<-y_x[,i] x<-colnames(y_x)

Hi, I am currently writing code to input a few thousand files, run them through the Random Forests package, and then output corresponding results. When I use the code below: zz<-textConnection("ex.lm.out", "w") sink(zz)

Dear R-Users, I have a question concerning the determination of breakpoints and comparison of slopes from broken-line regression models. Although this is rather a standard problem in data analysis, all information I gathered so far, did not answer my questions. I added a subsetted example of my data. Basically it is a timeseries of recorded phenotypes in three different groups of plants. You

...stat teaching I will include Rcommander (it indeed simplifies syntax problems that makes students frequently miss the core statistical problems). But I could not find how to make a simple chisquare comparison between observed frequencies and expected frequencies (eg in genetics where you expect phenotypic frequencies corresponding to 3:1 in standard dominant/recessif alleles). Any idea where this feature might be hidden? Or could it be added to Rcommander? Thanks, Christian. ps: in case I am not making myself clear, can Rcommander be made to perform > chisq.test(c(61,39),p=c(0.75,0.25))

...lection more flexible than "[" method . The schema I am thinking for is the following: subset.ExpressionSet <- function(x,subset,...){ } I will use the subset argument for rows (genes), as in default method. Now I would like to allow to select different columns (features) based on phenotypic data. phenotypic data provides detailed information about the columns. Basically, first function I have written allows the following: > sub1 <- subset(ExpressionSetObject, subset=NULL, V1=value1, v2=value2) # subset=NULL takes all rows See: there are two conditions on two variables belongi...

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: