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)
but only works for one assay in the list of 96. 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? Is this topic included in the posting guide?
--
View this message in context:
http://r.789695.n4.nabble.com/applying-cbind-or-any-function-across-all-components-in-a-list-tp4631128p4631260.html
Sent from the R help mailing list archive at Nabble.com.
______________________________________________
R-help@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.
