: arun
To: Vera Costa
Cc: R help
Sent: Thursday, March 28, 2013 2:28 PM
Subject: Re: [R] new question
Hi,
The function outputs the unique rows and also chisq test on frequency ( by row).
Spec <- function(lista,FDR_k) {
list.new<-lapply(lista,function(x) within(x,{spec<- as.character
help
Sent: Thursday, March 28, 2013 10:18 AM
Subject: Re: [R] new question
Hi,
Try this:
Spec <- function(lista,FDR_k) {
list.new<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))
split.list<-split(list.new,names(lista))
#Data needed with FDR
To: arun
Sent: Th
Hi,
Try this:
Spec <- function(lista,FDR_k) {
list.new<-lapply(lista,function(x) within(x,{spec<- as.character(spec)}))
split.list<-split(list.new,names(lista))
#Data needed with FDR
To: arun
Sent: Thursday, March 28, 2013 9:43 AM
Subject: Re: new question
I don't remove duplicated, but
Hi,
Regarding the first question:
ListFacGroup<- lapply(ListFacGroup,unique)
Spec(ListFacGroup,0.05)
#
# Seq Mod z a2 c2 c3 t2
#1 aAATATAGPR 1-n_acPro/ 2 1 0 0 1
#2 aAAASSPVGVGQR 1-n_ac
Hi,
Try this: (Used the old data folder)
Compares the spec counts of sub directory with each other.
directory<- "/home/arunksa111/dados"
GetFileList <- function(directory,number){
setwd(directory)
filelist1<-dir()[file.info(dir())$isdir]
direct<-dir(directory,pattern = paste("MSMS_",num
Hi,
Try this:
directory<- "/home/arunksa111/dados"
GetFileList <- function(directory,number){
setwd(directory)
filelist1<-dir()[file.info(dir())$isdir]
direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
direct<-lapply(direct,f
Sorry, I am not sure I understand your question.
You have 5 boxplots(if I remember correctly) on a single page and these 5
boxplots have titles "a1","a2","c1","c2","t1" (or something like that).
Could you try:
par(mfcol(c(3,2)) and see if that helps. (not tested)
A.K.
__
I deleted the 't' subfolders from the dados folder.
If you don't have 't' folders, wouldn't it be better to use:
directory<- "/home/arunksa111/dados"
FacGroup<-c(0,1,0,2,2,0,0)
#instead of
#FacGroup<-c(0,1,0,2,2,0,3)
FacGroup<-c(0,1,0,2,2,0,3)
lista[FacGroup!=0]
#[1] "/home/arunksa111/dados/
z.boxplot<- function(lst){
new.list<- lapply(lst,function(x) x[x$FDR<0.01,])
print(new.list)
par(mfrow=c(2,2))
b1<-lapply(names(new.list),function(x) lapply(new.list[x],function(y)
boxplot(FDR~z,data=y,xlab="Charge",ylab="FDR",main=x)))
}
z.boxplot(ListFacGroup) #prints new.list
If you
Hi,
Try this:
directory<- "/home/arunksa111/dados"
#modified the function
GetFileList <- function(directory,number){
setwd(directory)
filelist1<-dir()
lista<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = TRUE, recursive = TRUE)
output<- list(filelist
Hi,
directory<- "/home/arunksa111/dados" #renamed directory to dados
filelist<-function(directory,number,list1){
setwd(directory)
filelist1<-dir(directory)
direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
list1<-lapply(direct, func
Hi,
directory<- "/home/arunksa111/data.new"
#first function
filelist<-function(directory,number,list1){
setwd(directory)
filelist1<-dir(directory)
direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""),
full.names = FALSE, recursive = TRUE)
list1<-lapply(direct, function(x) rea
Yes,it works well.
Thanks for your help.
At 2011-12-14 13:06:14,"Jorge I Velez" wrote:
Hi lm_mengxin,
If that's the case, just use as.factor():
> fit <- glm(case ~ as.factor(induced) + as.factor(spontaneous),
> family=binomial, data=infert)
> logistic.display(fit)
According to the example of logistic.display:
model0 <- glm(case ~ induced + spontaneous, family=binomial, data=infert)
summary(model0)
logistic.display(model0)
induced: 3levels 0,1,2
spontaneous: 3levels 0,1,2
So if 0 is reference, we should get 2 OR for " induced1"," induced2","
spontane
Hi lm_mengxin,
If that's the case, just use as.factor():
> fit <- glm(case ~ as.factor(induced) + as.factor(spontaneous),
family=binomial, data=infert)
> logistic.display(fit)
OR lower95ci upper95ci Pr(>|Z|)
as.factor(induced)1 1.585398 0.7972313 3.1527
I forgot to mention (sorry for double posting) that str(infert) shows that
"induced" and "spontaneous" are not factors:
'data.frame': 248 obs. of 8 variables:
$ education : Factor w/ 3 levels "0-5yrs","6-11yrs",..: 1 1 1 1 2 2 2
2 2 2 ...
$ age : num 26 42 39 34 35 36 23 32 21 28
Hi,
Are you sure? That's not what I got:
> require(epicalc)
> ?logistic.display
> model0 <- glm(case ~ induced + spontaneous, family=binomial, data=infert)
> logistic.display(model0)
Logistic regression predicting case
crude OR(95%CI) adj. OR(95%CI)P(Wald's test)
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