Re: [R] Remove highly correlated variables from a data frame or matrix

Try hclust(as.dist(1-calc.rho), method = "average"). Peter On Fri, Nov 15, 2019 at 10:02 AM Ana Marija wrote: > > HI Peter, > > Thank you for getting back to me and shedding light on this. I see > your point, doing Jim's method: > > > keeprows<-apply(calc.rho,1,function(x) return(sum(x>0.8)<3))

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Re: [R] Glmnet survival cox predict

On 11/15/19 10:49 AM, Amir Hadanny wrote: Hi all, i'm trying to get the prediction probabilities for a survival elastic net. When i use try to predict using the train model on the test set, it creates an object with the number rows of the train data (6400 rows) instead of the test data (2400

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Hi all, i'm trying to get the prediction probabilities for a survival elastic net. When i use try to predict using the train model on the test set, it creates an object with the number rows of the train data (6400 rows) instead of the test data (2400 rows). I really don't understand why, and that

Re: [R] Remove highly correlated variables from a data frame or matrix

While the remedy for your dissatisfaction with my previous solution should be obvious, I will make it explicit. # that is rows containing at most one value > 0.8 # ignoring the diagonal keeprows<-apply(ro246,1,function(x) return(sum(x>0.8)<2)) ro246.lt.8<-ro246[keeprows,keeprows] Jim

Re: [R] Remove highly correlated variables from a data frame or matrix

if it is of any help my correlation matrix (calc.rho) was done here, under LDmatrix tab https://ldlink.nci.nih.gov/?tab=ldmatrix and dataset of 246 is bellow rs56192520 rs3764410 rs145984817 rs1807401 rs1807402 rs35350506 rs2089177 rs12325677 rs62064624 rs62064631 rs2349295 rs2174369 rs7218554

Re: [R] Remove highly correlated variables from a data frame or matrix

HI Peter, Thank you for getting back to me and shedding light on this. I see your point, doing Jim's method: > keeprows<-apply(calc.rho,1,function(x) return(sum(x>0.8)<3)) > ro246.lt.8<-calc.rho[keeprows,keeprows] > ro246.lt.8[ro246.lt.8 == 1] <- NA > (mmax <- max(abs(ro246.lt.8), na.rm=TRUE))