similar to: pheno package

Full_Name: Anja Eggert Version: 2.4.1 OS: Submission from: (NULL) (139.30.70.203) I want to install the pheno package. This is not working. What can I do? Thank you very much, Anja

Hello The other say I posted a question about altering confidence limits in the seqMK() function in the pheno package. I didn't get any bites but in any case I've been trying to use this function. It seems to me to give very odd results - sometimes identifying 8 or 9 changepoints in a relatively short vector of maybe 40 elements, and at other times not giving any changepoints at all,

Hello does anyone know how to set the confidence level within the seqMK() function in the pheno package. It seems to be set automatically at 0.05 and there seems to be neither an input function to set a different level, as there are with some changepoint functions, nor an output to give one the p-value of the changepoint identification which you get with functions ie func$p_value etc ... Thanks

Dear R users, This command works (calling a programm -called whap- with file specifiers etc.): >system('cmd /c "c:\\pheno\\whap --file c:\\pheno\\smri --alt 1 --perm 500"', intern=TRUE) Now I need to call it from a loop to replace the "1" by different number, however I get lost using the quotes: I tried numerous versions of: >i<-1

Hello, When programming it is better to use dat[["variable"]] than dat$variable. So your code could be pfas.pheno[[cat.var]] <- NA pfas.pheno[[cat.var]][pfas.pheno[,i] <= quantile(pfas.pheno[,i],0.25, na.rm =T)] <- 0 etc. Untested. Hope this helps, Rui Barradas On 4/19/2018 7:20 PM, Ding, Yuan Chun wrote: > Hi All, > > I want to create a categorical variable,

> On Apr 19, 2018, at 11:20 AM, Ding, Yuan Chun <ycding at coh.org> wrote: > > Hi All, > > I want to create a categorical variable, cat.pfoa, in the file of pfas.pheno (a data frame) based on log2pfoa values. I can do it using the following code. > > pfas.pheno <-within(pfas.pheno, {cat.pfoa<-NA > cat.pfoa[pfas.pheno$log2pfoa

Hi All, I want to create a categorical variable, cat.pfoa, in the file of pfas.pheno (a data frame) based on log2pfoa values. I can do it using the following code. pfas.pheno <-within(pfas.pheno, {cat.pfoa<-NA cat.pfoa[pfas.pheno$log2pfoa <=quantile(pfas.pheno$log2pfoa,0.25, na.rm =T)]<-0 cat.pfoa[pfas.pheno$log2pfoa >=quantile(pfas.pheno$log2pfoa,0.75, na.rm =T)]<-2

> On Apr 19, 2018, at 1:22 PM, David Winsemius <dwinsemius at comcast.net> wrote: > > >> On Apr 19, 2018, at 11:20 AM, Ding, Yuan Chun <ycding at coh.org> wrote: >> >> Hi All, >> >> I want to create a categorical variable, cat.pfoa, in the file of pfas.pheno (a data frame) based on log2pfoa values. I can do it using the following code.

I am trying to find a convenient way to control line colors when printing from a for loop using the lines command. Right now I have solved this by creating a colors vector that is refered to in the loop with index. However, the colors choosen here are just 1,2,3,4,5... I would like to get colors from the col = rainbow(x) that you can use in plot() and set the to be my number of lines (I think

Dear List Members, I have encountered two problems when using the step function to select models. To better illustrate the problems, attached is an R image which includes the objects needed to run the code attached. lm.data.frame have factor variables with 3 levels. The following run shows the first problem. AICs (* and **) are different. I noticed that the Df for rs13482096:rs13483699 is 4,

Dear List Members, I have encountered two problems when using the step function to select models. To better illustrate the problems, an R image (step.add1.test.RData) which includes the objects needed to run the code (step.add1.test.R) can be found at www.biostat.wisc.edu/~pwang/r-help/<http://www.biostat.wisc.edu/%7Epwang/r-help/> lm.data.frame have factor variables with 3 levels. The

The function heatmap() allows to specify row/column labels via the options labRow/labCol. From the code of heatmap(), I understand that when no labels are specified, the row/column labels (or indices) of the input matrix are taken as labels and re-ordered together with the rows and columns of the matrix before plotting, whereas labels supplied via labRow/labCol are plotted in the original order.

Full_Name: Anja von Heydebreck Version: 1.9.1 OS: Linux Submission from: (NULL) (155.250.128.25) I obtained a negative p-value from the fisher.test() function: > fisher.test(matrix(c(14576,3023,89,68),2), alternative="g")$p.value [1] -8.426593e-13 With R 1.8.1, I got a p-value of -6.239231e-12 for this example. Anja von Heydebreck

Hi, ? I am very new to R. So, pardon my dumb question. I was trying to write my own function to run a different model (perform an ordered logistic regression) using the example in website http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml But R returns a error `R Error in eval(expr, envir, enclos) : object 's' not found' when I run it. What am I doing wrong here? Here's

Full_Name: Anja von Heydebreck Version: 1.3.0 OS: Alpha Unix Submission from: (NULL) (141.14.19.61) Hi, I repeatedly obtained meaningless results from the function 'cutree' in the 'mva' package, when the argument 'h' was greater or equal to the maximum height occuring: > library('mva') > y [,1] [,2] [,3] [,4] [1,] 0 1 -1 1 [2,] 0 -1

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Dear R-help list, Apologies. I am trying to convert one table to another. It feels that it should be a very straightforward answer with a single (or two) commands with the right extensions, but I really can't figure this out right now. I have several hundred pheno factors actually, so manually doing this line by line is not an option. My original table is approximately like this : ID

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

hi all, I have a matrix and named each row and column as like below... a<-matrix(c(seq(3,45,3),seq(10,6,-1)),4,5,byrow=F) > col<-c("peter","david","richrd","vincent","selva") > rows<-c("julius","caeser","anja","maya") > dimnames(a)<-list(rows,col) > a peter david

Hi, I am running the 64bit version of R on a AIX RS6000 cluster on which is also running the ' SQL*Plus: Release 9.2.0.2.0' in the 'ORACLE-environment Version 64 bit AIX 5.1'. I have problems setting up an Oralce database connection. I can instantiate a driver using drv <- Oracle(). But when I try to connect to my database using dbConnect (dbConnect(drv,