Hi , I am new to R . I am facing difficulty how to make pairwise comparisions. For example. I have a file which looks like below a b c d x 3 6 7 6 y 7 8 6 5 z 5 4 7 8 Here I need to look for the each pairwise comparisions (ab,ac,ad,bc,bd,cd for each row) For instance ,looking at first row, for x i need to look for ab values and take the min(3,6) >5 ,if its satistfies the count should be noted, (now count is 0), bc values ,min(6,7) >5 ,count for x =1 etc. Likewise all the comparisons are made and count is noted for x,y,z. Is there any function to make pairwise comparisions in R or any easy way to do this? Any help is greatly appreciated. -- View this message in context: http://r.789695.n4.nabble.com/pairwise-comparisions-tp4642656.html Sent from the R help mailing list archive at Nabble.com.
pairwise comparisions
5 messages · priya, Bert Gunter, David Winsemius +1 more
1. Be forewarned: There may be special approaches built into specific packages that are better than "generalist" approaches like the one I suggest here. 2. The general approach to this sort of thing is with ?outer, if I understand you correctly. 3. Have you read an Introduction to R (ships with every copy of R)? If not, stop and read it before posting further to this list, as it may well contain answers to the questions you wish to pose here. Cheers, Bert
On Mon, Sep 10, 2012 at 7:00 AM, priya <jaggari_ash at yahoo.co.in> wrote:
Hi , I am new to R . I am facing difficulty how to make pairwise comparisions. For example. I have a file which looks like below a b c d x 3 6 7 6 y 7 8 6 5 z 5 4 7 8 Here I need to look for the each pairwise comparisions (ab,ac,ad,bc,bd,cd for each row) For instance ,looking at first row, for x i need to look for ab values and take the min(3,6) >5 ,if its satistfies the count should be noted, (now count is 0), bc values ,min(6,7) >5 ,count for x =1 etc. Likewise all the comparisons are made and count is noted for x,y,z. Is there any function to make pairwise comparisions in R or any easy way to do this? Any help is greatly appreciated. -- View this message in context: http://r.789695.n4.nabble.com/pairwise-comparisions-tp4642656.html Sent from the R help mailing list archive at Nabble.com.
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
On Sep 10, 2012, at 7:00 AM, priya wrote:
Hi , I am new to R .
How new? Is this still in a file? ... or has it been imported to an R object. If it really still is in a file, then Bert's suggestion of first reading "Intro to R" rather than posting to R help is on point. If it is an R object, you _should_ have used dput(head(obj)) to provide an appropriate test case for solutions.
I am facing difficulty how to make pairwise comparisions. For example. I have a file which looks like below a b c d x 3 6 7 6 y 7 8 6 5 z 5 4 7 8 Here I need to look for the each pairwise comparisions (ab,ac,ad,bc,bd,cd for each row)
Let's assume it's in a matrix of data.frame named X. To get pairwise combinations try: CX <- combn( colnames(X), 2) That's going to be a 2 row character matrix. Perhaps this will work but since you provide not example it will remain untested. apply(CX, 2, function(comb), pmin(X[, comb[1]], X[, comb[2]] ) )
For instance ,looking at first row, for x i need to look for ab values and take the min(3,6) >5 ,if its satistfies the count should be noted, (now count is 0), bc values ,min(6,7) >5 ,count for x =1 etc. Likewise all the comparisons are made and count is noted for x,y,z. Is there any function to make pairwise comparisions in R or any easy way to do this? Any help is greatly appreciated.
David Winsemius, MD Alameda, CA, USA
On Sep 10, 2012, at 11:03 AM, David Winsemius wrote:
On Sep 10, 2012, at 7:00 AM, priya wrote:
Hi , I am new to R .
How new? Is this still in a file? ... or has it been imported to an R object. If it really still is in a file, then Bert's suggestion of first reading "Intro to R" rather than posting to R help is on point. If it is an R object, you _should_ have used dput(head(obj)) to provide an appropriate test case for solutions.
I am facing difficulty how to make pairwise comparisions. For example. I have a file which looks like below a b c d x 3 6 7 6 y 7 8 6 5 z 5 4 7 8 Here I need to look for the each pairwise comparisions (ab,ac,ad,bc,bd,cd for each row)
Let's assume it's in a matrix of data.frame named X. To get pairwise combinations try: CX <- combn( colnames(X), 2) That's going to be a 2 row character matrix. Perhaps this will work but since you provide not example it will remain untested. apply(CX, 2, function(comb), pmin(X[, comb[1]], X[, comb[2]] ) )
The virtues of testing herein demonstrated. There is an inappropriately placed comma right after function(comb)
X <- read.table(text=" a b c d
+ x 3 6 7 6 + y 7 8 6 5 + z 5 4 7 8", header=TRUE)
CX <- combn( colnames(X), 2) apply(CX, 2, function(comb) pmin(X[, comb[1]], X[, comb[2]] ) )
[,1] [,2] [,3] [,4] [,5] [,6] [1,] 3 3 3 6 6 6 [2,] 7 6 5 6 5 5 [3,] 4 5 5 4 4 7
For instance ,looking at first row, for x i need to look for ab values and take the min(3,6) >5 ,if its satistfies the count should be noted, (now count is 0), bc values ,min(6,7) >5 ,count for x =1 etc. Likewise all the comparisons are made and count is noted for x,y,z. Is there any function to make pairwise comparisions in R or any easy way to do this? Any help is greatly appreciated.
--
David Winsemius, MD Alameda, CA, USA
HI,
Sorry, there was a mistake.? I forgot to add some code.
Try this:
dat1<-read.table(text="
?? a b c d
x? 3 6 7 6
y? 7 8 6 5
z? 5 4 7 8
",sep="",header=TRUE)
new1<-sapply(combn(dat1[,1:4],2),`[`,1:3)
?colnames(new1)<-sapply(combn(colnames(dat1),2),`[`,1)
new2<-as.matrix(new1)
?dim(new2)<-c(3,2,6)
list1<-do.call(list,lapply(1:dim(new2)[3],function(i) new2[,,i]))
reslist1<-lapply(list1,function(x) apply(x,1,function(x) ifelse(min(x[1],x[2])>5,1,0)))
names(reslist1)<-c("ab","ac","ad","bc","bd","cd")
res<-data.frame(counts=apply(do.call(cbind,reslist1),1,sum))
?row.names(res)<-row.names(dat1)
?res
#? counts
#x????? 3
#y????? 3
#z????? 1
A.K.
----- Original Message -----
From: David Winsemius <dwinsemius at comcast.net>
To: priya <jaggari_ash at yahoo.co.in>
Cc: r-help at r-project.org
Sent: Monday, September 10, 2012 2:03 PM
Subject: Re: [R] pairwise comparisions
On Sep 10, 2012, at 7:00 AM, priya wrote:
Hi , I am new to R .
How new? Is this still in a file? ... or has it been imported to an R object. If it really still is in a file,? then Bert's suggestion of first reading "Intro to R" rather than posting to R help is on point. If it is an R object, you _should_ have used dput(head(obj)) to provide an appropriate test case for solutions.
I am facing difficulty how to make pairwise comparisions. For example. I have a file which looks like below ? a b c d x? 3 6 7 6 y? 7 8 6 5 z? 5 4 7 8 Here I need to look for the each pairwise comparisions (ab,ac,ad,bc,bd,cd for each row)
Let's assume it's in a matrix of data.frame named X. To get pairwise combinations try: CX <- combn( colnames(X), 2) That's going to be a 2 row character matrix. Perhaps this will work but since you provide not example it will remain untested. apply(CX, 2, function(comb), pmin(X[, comb[1]], X[, comb[2]] ) )
For instance ,looking at first row, for x i need to look for ab values and take the min(3,6) >5 ,if its satistfies the count should be noted, (now count is 0), bc values ,min(6,7) >5 ,count for x =1 etc. Likewise all the comparisons are made and count is noted for x,y,z. Is there any function to make pairwise comparisions in R or any easy way to do this? Any help is greatly appreciated.
David Winsemius, MD Alameda, CA, USA ______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.