search for: pheno

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...

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, cat.pfoa, in the file of p...

> 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$log2pfoa <=quantile(pfas.pheno$log2pfoa,0.25, na.rm =T)]<-0 > cat.pfoa[pfas.pheno$log2pfoa >=quantile(pfas.pheno$log2p...

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 >system(paste(c("'cmd /c "c:\\pheno\\wha...

...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. >> >> 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(pf...

...to my number of lines, but I don't know how to implement this into my loop. Is this possible? This is my script: __________________________________________________________________ ###creating two emty vectors and opening a graphics window x <- vector() y <- vector() plot(x,y, xlim = c(pheno.dt$year[1],pheno.dt$year[nrow(pheno.dt)]), ylim = c(min(pheno.dt$julian, na.rm = TRUE),max(pheno.dt$julian, na.rm = TRUE)), xlab = "Year", ylab = "Julian Day") ###setting up colors sp_pheno.unique <- unique(pheno.dt$sp_pheno) colors <- seq(1,200,1) ####printloop...

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 1 A Breast Cancer 2 A Appendicitis 3 A Microcephaly 4 B Polyps 5 B Autism 6 C Autism 7 D Breast Cancer 8 D Polyp...

...om rs13483699 and 4 from interactions. When I ran add1 directly, I got Df=6 and AIC 848.75. > step2.bic.out <- step(step.bic.out, scope=list(lower=scope.lower2, upper=scope.upper2), + direction="both", k=log(length(step.bic.out$y)), trace=1) Start: AIC=841.18 pheno.dat ~ rs13479085 + rs13480057 + rs13482096 + rs8254221 Df Deviance AIC + rs13482096:rs13483699 4 216.63 840.63 (*) <none> 233.82 841.18 - rs8254221 2 244.08 842.90 - rs13482096 2 245.20 844.31 ...... Step: AIC=...

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

...ssion) 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 what I got from the debug file. # Input data n <- 10 PHENO <- c( 1, 3, 2, 3, 1, 1, 1, 2, 1, 2 ) c <- c( 1, 1, 0, 0, 0, 0, 0, 1, 0, 0 ) COVAR <- matrix( c , nrow = n , byrow=T) CLUSTER <- c( 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ) l <- 22 g <- c( 0, 1, 1, 0, 0, 0, 1, 0, 2, 1, 0, 0, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 1, 2, 0, 0, 0, 2, 0, 0, 0, 1, 0, 1...

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, Anj...

...om rs13483699 and 4 from interactions. When I ran add1 directly, I got Df=6 and AIC 848.75. > step2.bic.out <- step(step.bic.out, scope=list(lower=scope.lower2, upper=scope.upper2), + direction="both", k=log(length(step.bic.out$y)), trace=1) Start: AIC=841.18 pheno.dat ~ rs13479085 + rs13480057 + rs13482096 + rs8254221 Df Deviance AIC + rs13482096:rs13483699 4 216.63 840.63 (*) <none> 233.82 841.18 - rs8254221 2 244.08 842.90 - rs13482096 2 245.20 844.31 ...... Step: AIC=...

...ject shortened manually -- to pass anti-spam filters Original-subject: Incorrect matrix of spearman correlations working \ large (24000 by 425 and 78 by 425 data frames) in 64-bit Linux machines;\ the same code gives correct results in 32-bits Win and Mac (PR#9568) }} cc_s<-cor(phenos,vec,method="spearman",use="pairwise.complete.obs") this is a line copied from real script producing different results in 64 bit/Linux/R (wrong) and Mac&Win (correct) The script was implemented on 4 machines with Linux 64, Suse 9-10, in 5 variants of R -- versions from 2.3...

>>>>>>>>>>>>>>><<<<<<<<<<<<<<<< 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 you have an up-to-date version...

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 ... Tha...

...uot;)) I get the message: Error in oraNewConnection(drv, ...) : RS-DBI driver: (ORA-12154: TNS:could not resolve service name) When I use oraNewConnection (oraNewConnection(drv,username="xxx", password="xxx")) I get the message: Error in oraNewConnection(drv, username = "pheno", password = "pheno") : RS-DBI driver: (ORA-12541: TNS:no listener) However, sqlplus works well and the listener is also running. Any idea what could be the problem here? joerg

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 < 3 chi-squared = 0.2268, df = 1, p-value = 0.6339 > tabletrend(with(dat2, table(pheno, geno))) [1] 0.6338308 -------- Message...

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), genoty...

...s anti-spam filters > > Original-subject: Incorrect matrix of spearman correlations working \ > large (24000 by 425 and 78 by 425 data frames) in 64-bit Linux machines;\ > the same code gives correct results in 32-bits Win and Mac (PR#9568) > }} > > cc_s<-cor(phenos,vec,method="spearman",use="pairwise.complete.obs") > > this is a line copied from real script producing different results in 64 > bit/Linux/R (wrong) and Mac&Win (correct) > > The script was implemented on 4 machines with Linux 64, Suse 9-10, in 5 variants &g...

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, despite visu...