similar to: color of lines while printing through for loop

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.

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, we are using samba 3.0.10-17 with openlddap 2.2.6-37.22 as backend. We use roaming profiles, but because of problems with different operating systems and the profile size, we want to use locale profiles. I tried to change logon path in smb.conf in an emty string, but no changes, if I delete this entry in smb.conf, samba use a default value and this is on the server. So I tried to change

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

>>>>>>>>>>>>>>><<<<<<<<<<<<<<<< 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 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

Hi, I have imported some sasdata into R using the sas7bdat package. I have some nominal variables with some missing values. R is creating a new level which is emty ??.When I ask for tabulate this new level is presented with 0 as a frequency. I want to get rid of this level and have my file imported correctly. Do you have some hint to help solve this problem? Please use this email adress to

Hi, I have imported some sasdata into R using the sas7bdat package. I have some nominal variables with some missing values. R is creating a new level which is emty ??.When I ask for tabulate this new level is presented with 0 as a frequency. I want to get rid of this level and have my file imported correctly. Do you have some hint to help solve this problem? Please use this email adress to

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

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,

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

i have two RData files,,i want to print them to check the format of the tables in these files,,,i can load both the files and can read it as well > load('ann.RData') > str(ann) List of 4 $ Name : chr [1:561466] "rs3094315" "rs12562034" "rs3934834" "rs9442372" ... $ Position : int [1:561466] 742429 758311 995669 1008567 1011278 1011521