Re: [R] help with parsing multiple coxph() results
Thanks, I can do calculatation for each gene, however what I want to do is to fit the model on each and every gene, store their result and then be able to access all of them, then filter on them, to do that: 1. I need to know how to access each part of the coxph result, like its coefficient, exp(coef),P,Z, etc. 2. I need to be able to generate a graphical presentation of the filtered genes, to show how their expression level is associated with survival, etc. I just could not find any explanation as to how to check different part of a coxph result, not to mention to store them in certain data structure, like vectors Java or Perl, etc. Best Hao -Original Message- From: Fredrik Lundgren [mailto:[EMAIL PROTECTED] Sent: Tuesday, January 17, 2006 2:26 PM To: Hao Liu Cc: R-help Subject: Re: [R] help with parsing multiple coxph() results Hao, I'm not sure but you have specified your modell as tautology. The formula below should be enough: survtest <- coxph(Surv(fup_interval, endpoint) ~ geneid, data = pcc.primary.stg.3.cox) HTH Fredrik - Original Message - From: "Hao Liu" <[EMAIL PROTECTED]> To: Sent: Tuesday, January 17, 2006 7:47 PM Subject: [R] help with parsing multiple coxph() results > Dear All: > > I have a question on using coxph for multiple genes: > > I have written code to loop through all 22283 genes in the Hgu-133A > and > apply coxph on survival data. > > However, I don't know how to work with the result for each gene: > > survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg. > 3.cox[,'endpoint'])~pcc.primary.stg.3.cox[,'geneid'],pcc.primary.stg.3.cox) > > each time I tried to look at what is in survtest it gives me this: > > > == > coxph(formula = Surv(pcc.primary.stg.3.cox[, "fup_interval"], >pcc.primary.stg.3.cox[, "endpoint"]) ~ pcc.primary.stg.3.cox[, >"208181_at"], data = pcc.primary.stg.3.cox) > > > coef exp(coef) se(coef) z > p > pcc.primary.stg.3.cox[, "208181_at"] -1.87 0.1540.688 -2.72 > 0.0065 > > Likelihood ratio test=8.56 on 1 df, p=0.00343 n= 48 > > === > > What I wanted to do is to use a matrix to store each "survtest" > result, but > it seems to me there is no data > structure in R to store the result of coxph into a matrix. I got the > following code to calculate a P value > based on "survtest" > = > z<-survtest$coefficients/sqrt(surv$var) > p<-2*(1-pnorm(abs(z))) > > then, what is the P value thus calculated? > === > The question I have are: > > 1. How do I access different parts of coxph result? > 2. Is there a way to store multiple coxph results into a data > structure that > can be efficiently accessed? > 3. if I find a list of genes I am interested, are there efficient to > plot > all of them based on the survial data? > > Thanks > Hao Liu, Ph. D > > > > [[alternative HTML version deleted]] > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] help with parsing multiple coxph() results
Thanks for your reply, but I am not sure if I understand your reply right: are you saying the "geneid" in your post is a vector of all 22283 genes? I want to do cox fit to each and everyone of the 22283 genes and need a way to summarize it -- to do that, I need to know how to parse the result for each coxph result. Thanks Hao [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] help with parsing multiple coxph() results
Hao, I'm not sure but you have specified your modell as tautology. The formula below should be enough: survtest <- coxph(Surv(fup_interval, endpoint) ~ geneid, data = pcc.primary.stg.3.cox) HTH Fredrik - Original Message - From: "Hao Liu" <[EMAIL PROTECTED]> To: Sent: Tuesday, January 17, 2006 7:47 PM Subject: [R] help with parsing multiple coxph() results > Dear All: > > I have a question on using coxph for multiple genes: > > I have written code to loop through all 22283 genes in the Hgu-133A > and > apply coxph on survival data. > > However, I don't know how to work with the result for each gene: > > survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg. > 3.cox[,'endpoint'])~pcc.primary.stg.3.cox[,'geneid'],pcc.primary.stg.3.cox) > > each time I tried to look at what is in survtest it gives me this: > > > == > coxph(formula = Surv(pcc.primary.stg.3.cox[, "fup_interval"], >pcc.primary.stg.3.cox[, "endpoint"]) ~ pcc.primary.stg.3.cox[, >"208181_at"], data = pcc.primary.stg.3.cox) > > > coef exp(coef) se(coef) z > p > pcc.primary.stg.3.cox[, "208181_at"] -1.87 0.1540.688 -2.72 > 0.0065 > > Likelihood ratio test=8.56 on 1 df, p=0.00343 n= 48 > > === > > What I wanted to do is to use a matrix to store each "survtest" > result, but > it seems to me there is no data > structure in R to store the result of coxph into a matrix. I got the > following code to calculate a P value > based on "survtest" > = > z<-survtest$coefficients/sqrt(surv$var) > p<-2*(1-pnorm(abs(z))) > > then, what is the P value thus calculated? > === > The question I have are: > > 1. How do I access different parts of coxph result? > 2. Is there a way to store multiple coxph results into a data > structure that > can be efficiently accessed? > 3. if I find a list of genes I am interested, are there efficient to > plot > all of them based on the survial data? > > Thanks > Hao Liu, Ph. D > > > > [[alternative HTML version deleted]] > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] help with parsing multiple coxph() results
Dear All: I have a question on using coxph for multiple genes: I have written code to loop through all 22283 genes in the Hgu-133A and apply coxph on survival data. However, I don't know how to work with the result for each gene: survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg. 3.cox[,'endpoint'])~pcc.primary.stg.3.cox[,'geneid'],pcc.primary.stg.3.cox) each time I tried to look at what is in survtest it gives me this: == coxph(formula = Surv(pcc.primary.stg.3.cox[, "fup_interval"], pcc.primary.stg.3.cox[, "endpoint"]) ~ pcc.primary.stg.3.cox[, "208181_at"], data = pcc.primary.stg.3.cox) coef exp(coef) se(coef) z p pcc.primary.stg.3.cox[, "208181_at"] -1.87 0.1540.688 -2.72 0.0065 Likelihood ratio test=8.56 on 1 df, p=0.00343 n= 48 === What I wanted to do is to use a matrix to store each "survtest" result, but it seems to me there is no data structure in R to store the result of coxph into a matrix. I got the following code to calculate a P value based on "survtest" = z<-survtest$coefficients/sqrt(surv$var) p<-2*(1-pnorm(abs(z))) then, what is the P value thus calculated? === The question I have are: 1. How do I access different parts of coxph result? 2. Is there a way to store multiple coxph results into a data structure that can be efficiently accessed? 3. if I find a list of genes I am interested, are there efficient to plot all of them based on the survial data? Thanks Hao Liu, Ph. D [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
