[R] applying cbind (or any function) across all components in a list

[Rui Barradas]

Hello,

Let me give it a try.
This last post made it clear, I hope. I have two interpretations of your 
problem.

1. 'l1' only has three columns, corresponding to clusters (genotypes) 
XX, XY and YY, and 'l2' has one less column, corresponding to the 
midpoints between their closest genotype cluster.

2. 'l1' can have any number of columns and 'l2' is the same as above, 
i.e., has one less column.

In any case, the result is not the pairwise products of all possible 
combinations of columns of 'l1' and 'l2' matrices, but only those at a 
certain distance. In this case, fun2 below is more general.

fun1 <- function(x, y){
     cbind((x[, 1] + y[, 1])/2, (x[, 2] + y[, 1])/2,
         (x[, 2] + y[, 2])/2, (x[, 3] + y[, 2])/2)
}


fun2 <- function(x, y){
     midpoint <- function(i, j) (x[, i] + y[, j])/2

     colx <- ncol(x)
     res <- matrix(nrow = nrow(x), ncol = 2*colx - 2)
     k <- 1
     res[, k] <- midpoint(1, 1)
     for(cx in seq_len(colx)[-c(1, colx)])
         for(dist in 1:0)
             res[, k <- k + 1] <- midpoint(cx, cx - dist)
     res[, k + 1] <- midpoint(colx, colx - 1)
     res
}

lapply(seq_len(length(l1)), function(i) fun1(l1[[i]], l2[[i]]))
lapply(seq_len(length(l1)), function(i) fun2(l1[[i]], l2[[i]]))


If I'm wrong, sorry for the mess.

Rui Barradas


Em 25-05-2012 11:00, r-help-request at r-project.org escreveu:
> Date: Thu, 24 May 2012 15:37:51 -0700 (PDT)
> From: Hans Thompson<hans.thompson1 at gmail.com>
> To:r-help at r-project.org
> Subject: Re: [R] applying cbind (or any function) across all
> 	components in a list
> Message-ID:<1337899071674-4631260.post at n4.nabble.com>
> Content-Type: text/plain; charset=us-ascii
>
> 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.
>
>