On May 24, 2012, at 6:37 PM, Hans Thompson wrote:
The function I am giving for context is cbind. Are you asking how I
would
like to apply the answer to my question?
I am trying to take the results of a Fluidigm SNP microarray,
organized by
assay into a list (each component is the results of one assay), find
coordinate midpoints ([1,] and [2,] of my XX, XY, and YY clusters
(these are
genotypes) and is represented by l1. l2 is the midpoint between XX/
XY and
XY/YY although I did not give this in my example for simplicity, and
I am
now trying to find the midpoint between these new midpoints and their
closest genotype clusters. This is represented as
cbind( l1[[1]][,1]+l2[[1]][,1])/2, (l1[[1]][,2]+l2[[1]][,1])/2,
(l1[[1]][,2]+l2[[1]][,2])/2, (l1[[1]][,3]+l2[[1]][,2])/2 )
cbind would not be much different than c() in this case.
but only works for one assay in the list of 96.
It's not really a function, but rather an expression that will be
evaluated. If you had a function it might look like :
bindfn <- function(l1, l1) { c( l1[[1]][,1]+l2[[1]][,1])/2, (l1[[1]][,
2]+l2[[1]][,1])/2,
(l1[[1]][,2]+l2[[1]][,2])/2, (l1[[1]][,3]+l2[[1]][,2])/2 ) }
And you could perhaps (depending on whether l1 and l2 were
constructed) properly execute:
do.call(bindfn, list(l1,l2))
perhaps:
mapply(bindfn, l1, l2)
You posted an example higher up in the thread but my wife is calling
me to dinner. Will return later.
I want to apply this to the
entire list. My entire code so far is:
## OPEN .CSV and ORGANIZE BY ASSAY
file=""
{
rawdata <- read.csv(file, skip = 15)
OrgAssay <- split(rawdata, rawdata$Assay)
## RETURN MIDPOINTS FOR EACH CLUSTER WITHOUT NO CALLS
#for loop
ClustMidPts <-list()
for(locus in 1:length(names(OrgAssay))){
ClustMidPts[[locus]]<-t(cbind(tapply(OrgAssay[[locus]][,"Allele.X.
1"],
OrgAssay[[locus]][,"Final"], mean,na.rm=T),
tapply(OrgAssay[[locus]][,"Allele.Y.1"],
OrgAssay[[locus]][,"Final"], mean,na.rm=T)))}
names(ClustMidPts)=names(OrgAssay)
## CREATE CLUSTER-CLUSTER MIDPOINT
#for loop
ClustClustMidPts <- list()
for(locus in 1:length(names(ClustMidPts))){
ClustClustMidPts[[locus]] <-
cbind(XXYX=(ClustMidPts[[locus]][,"XX"]+ClustMidPts[[locus]][,"YX"])/
2,
YXYY=(ClustMidPts[[locus]][,"YX"]+ClustMidPts[[locus]][,"YY"])/2)
}
names(ClustClustMidPts)=names(ClustMidPts)
Please also let me know how I messed up the formatting because it
shows up
fine in gmail even when I post on Nabble. How did I assume you were
using
Nabble?
Because you included no context. We cannot see your earlier postings.
Expecting us to page out to Nabble or refer back to other item s in
the thread is considered presumptuous on your part.
Is this topic included in the posting guide?
YES. It is. And you were asked to read the Posting Guide about 10
times by now.
--
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Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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David Winsemius, MD
West Hartford, CT
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
