search for: tumor

Displaying 17 results from an estimated 17 matches for "tumor".

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2017 Jul 12
1
submitting R scripts with command_line_arguments to PBS HPC clusters
...k to see if arguments are passed. > if(length(args)==0){ > stop("no args specified") > } > ## Then cycle through each element of the list and evaluate the expressions. > for(i in 1:length(args)){ > print(args[[i]]) > eval(parse(text=args[[i]])) > } > print(TUMOR) > print(GERMLINE) > print(CHR) qsub shell script test.sh: > #!/bin/bash > > #Note: the single quote '...' around the --args ... "..." "..." is important! > R CMD BATCH --no-save --no-restore '--args TUMOR="tumor.bam" GERMLINE...
2017 Jul 12
1
submitting R scripts with command_line_arguments to PBS HPC clusters
...brevity. On July 11, 2017 5:25:20 PM PDT, Bogdan Tanasa <tanasa at gmail.com> wrote: >Dear all, > >please could you advise me on the following : I've written a R script >that >reads 3 arguments from the command line, i.e. : > >" args <- commandArgs(TRUE) >TUMOR <- args[1] >GERMLINE <- args[2] >CHR <- args[3] ". > >when I submit the R script to a PBS HPC scheduler, I do the following >(below), but ... I am getting an error message. >(I am not posting the error message, because the R script I wrote works >fine when it is r...
2011 Feb 21
9
Interpreting the example given by Prof Frank Harrell in {Design} validate.cph
Dear R-help, I am having a problem with the interpretation of result from validate.cph in the Design package. My purpose is to fit a cox model and validate the Somer''s Dxy. I used the hypothetical data given in the help manual with modification to the cox model fit. My research problem is very similar to this example. This is the model without stratification: > library(Design)
2011 Feb 19
0
contrasting Somer's D from Design package
...ox model to my data and validate the Somer''s Dxy using the Design package. (Because of computation time problem, i only try 10 bootstrap samples for the time being) This is the model without stratification: > library(Design) > cox1a<-cph(surv.obj~factor(ecog)+factor(grade)+factor(tumor)+factor(extra),x=T,y=T) > coef1a<-coef(cox1a) > coef1a ecog=1 ecog=2 grade=2 grade=3 tumor=2 tumor=3 extra=1 0.3578954 0.8993140 0.4834090 0.5716166 0.7600330 1.5974558 0.8112942 > validate(cox1a,dxy=T,method="b",B=10)...
2017 Jul 12
1
submitting R scripts with command_line_arguments to PBS HPC clusters
Dear all, please could you advise me on the following : I've written a R script that reads 3 arguments from the command line, i.e. : " args <- commandArgs(TRUE) TUMOR <- args[1] GERMLINE <- args[2] CHR <- args[3] ". when I submit the R script to a PBS HPC scheduler, I do the following (below), but ... I am getting an error message. (I am not posting the error message, because the R script I wrote works fine when it is run from a regular terminal ....
2007 Nov 01
1
Help me in Cochran armitage trend test Coding
...d by ''coin'' could not be found In addition: Warning messages: 1: package ''coin'' was built under R version 2.6.0 2: package ''survival'' was built under R version 2.5.1 3: package ''mvtnorm'' was built under R version 2.5.1 > lungtumor <- data.frame(dose = rep(c(0, 1, 2), c(40, 50, 48)), + tumor = c(rep(c(0, 1), c(38, 2)), + rep(c(0, 1), c(43, 7)), + rep(c(0, 1), c(33, 15)))) > table(lungtumor$dose, lungtumor$tumor) 0 1 0 38 2 1 43 7 2 33 15 > independence_test(tumor ~ dose, data = lungtumor, teststat = &q...
2011 Oct 04
2
Assigning genes to CBS segmented output:
Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Samp...
2010 Jun 17
5
Problems using allEffects() (package effect)
Dear R users, I have some trouble using the allEffects() function to compute and display effect plots for a linear model. My data is quite simple, it concerns effects of 3 treatments on the tumoral volume of mice. vTum codes for the qualitative initial volume, from small to big, temps is the time in month since beginning of treatment, and S?rie codes for the batch. Data is unbalanced. > head(data) Id S?rie Traitement vTum temps Volume 55656.1 55656 7 3 1 1...
2011 Feb 24
3
accuracy of measurements
Dear R people Could you please help with following Trying to compare accuracy of tumor size evaluation by different methods. So data looks like id true metod1 method2 ... 1 2 2 2.5 2 1.5 2 2 3 2 2 2 etc. Could you please give a hint how to deal with that. Seems like {merror} does not suite to me because I am trying to compare accuracy of measurements with their true known valu...
2017 Jun 19
1
mixed models lmer function help!!
Hi,I have tumor growth curve data for a bunch of different mice in various groups. I want to compare the growth curves of the different groups to see if timing of drug delivery changed tumor growth.I am trying to run a mixed models with repeated measures over time with each mouse as a random effect with linear and...
2009 Feb 09
1
XML package- accessing nodes based on attributes
...331_251469343372_S01_CGH-v4_10_Apr08.txt"/> <Characteristic Type ="Patient" eName="PatientReference" eValue="TCGA-06-0875-01A"/> <Characteristic Type ="Patient" eName="SampleType" eValue="TUMOR"/> <Characteristic Type ="Patient" eName="SampleMarker" eValue="cy3"/> <Characteristic Type ="Patient" eName="PatientDateOfBirth" eValue="080808"/> <Charact...
2005 Jul 28
4
Cochran-Armitage-trend-test
Hi! I am searching for the Cochran-Armitage-trend-test. Is it included in an R-package? Thank you! --
2005 Feb 10
1
rats in survival package
...isters, Does anybody know what is the correct source of "rats" dataset in survival package? The help gives the following information: Rat data from survival5 Description: 48 rats were injected with a carcinogen, and then randomized to either drug or placebo. The number of tumors ranges from 0 to 13; all rats were censored at 6 months after randomization. Usage: data(rats) Format: rat: id rx: treatment,(1=drug, 0=control) observation: within rat start: entry time stop: exit time status:...
2007 Jun 14
1
Wilcoxon test on data matrix
Dear everyone, I am trying to do a Wilcoxon one-sided test on my gene expression data. These are the data i have in R: data.matrix (matrix, numeric) containing all gene expression data (42 rows=genes, 42 columns=tumors), no column header or row names data.cl (vector, numeric) consisting of 42 0''s and 1''s to indicate class 0 or class 1 for each column in data.matrix I want to do a Wilcoxon one-sided test on the data from class 0 versus the data from class 1, for each row (gene) of the data set....
2006 Apr 27
0
package pamr: pamr.adaptthresh() error rates
...ry(base) library(graphics) library(pamr) rm(list = ls()) gc() makeColon <- function(){ # This dataset has 24 cancer, and 9 normal samples n2 <- read.table("data/Colon.data",header = FALSE,sep = ",") cancdat <- n2[,n2[1,]== ''tumor''] normdat <- n2[,n2[1,]== ''normal''] cancdat <- cancdat[-1,] normdat <- normdat[-1,] mat <- as.matrix(cbind(cancdat,normdat)) actclass <- rep(c(1, 2), c(ncol(cancdat), ncol(normdat))) return(list(mat,actclass)) } m...
2017 Jul 28
0
Need help on the Lasso cox model with discrete time
Hi everyone, We have been trying to construct a Lasso-cox model with discrete time. We conducted follow-up examinations on the epileptic attack after tumor surgical resection among glioma patients. The patients are followed-up in the 6/12/24 months after surgical resection, which makes the epilepsy-free time discrete (6/12/24 months). We calcluated many features from the T2-images collected prior to surgical resection. We aimed to...
2004 Sep 28
4
Validating a Cox model on an external set
Good morning, Sorry to trouble the list. I have a problem I hope to seek your advice on. Essentially, I am trying to ''validate'' a multivariate Cox proportional hazards model built in a training set, by testing it on an external test set. I have performed a survfit using the Cox model to predict survival for the test set, and obtained individual predictions for survival