similar to: seqMK function

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,

Dear R-people, I tried to use a command seqMK(x) of the pheno package. However, the installation of the package fails with following error message: Error in library(pkg, character.only = TRUE) : 'pheno' is not a valid package -- installed < 2.0.0? What is the matter? Can anybody help me? I installed the latest version of R. Cheers, Anja --

Hello Does anyone know how to get the p values for changepoints in the "changepoint" package? There is guidance in the CRAN vignette https://cran.r-project.org/web/packages/changepoint/changepoint.pdf but I can't make it work to get the p value out... Thanks Nick Wray [[alternative HTML version deleted]]

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,

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 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

> 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 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

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,

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

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

Hi there, I'm trying to apply the Mann Kendall test for trend analysis of a time series. I have downloaded and installed the package Kendall and subsequently loaded it into the software. My time series is a .txt file with 2 columns - column 1 is the year (1985 - 2009) and column 2 is the corresponding entry variable. According to the R guidelines, the call should be: MannKendall(x)

Hi, I am running a correlation analysis on a temporal dataset. I was wondering if you would receive the same tau and p values running the function: MannKendall(x), where x is the dependant variable that changes with time as you would running: Kendall(d,x), where x is the exact same dataset as the x entered into MannKendall and d is the date on which the observation was made (assuming that

>>>>>>>>>>>>>>><<<<<<<<<<<<<<<< Pheno-Mint upsmon # /sbin/upsdrvctl start Network UPS Tools - UPS driver controller 2.6.1 Network UPS Tools - Generic HID driver 0.35 (2.6.1) USB communication driver 0.31 This PowerCOM device (0d9f:0004) is not (or perhaps not yet) supported by usbhid-ups. Please make sure

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

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,

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 UseR, I get an error when I run "R CMD check" on my .tar.gz file package, and I don't understand why since I don't obtain any error with "R CMD check" on the package directory. Do you have any idea ? $ sudo ./R-2.11.0/bin/R CMD check eqtl_1.1.tar.gz and $ sudo ./R-2.11.0/bin/R CMD --check-subdirs=no eqtl_1.1.tar.gz return an Error * checking for working

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the