R help - May 2012 - applying cbind (or any function) across all components in a list

#If I have two lists as follows

a1<-  array(1:6, dim=c(2,3))
a2<-  array(7:12, dim=c(2,3))
l1<-  list(a1,a2)



a3<-  array(1:4, dim=c(2,2))
a4<-  array(5:8, dim=c(2,2))
l2<-  list(a3,a4)


#how can I create a new list with the mean across all arrays within the
list, so all components are included?  As an example for [[1]];

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)



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The combination of column means in cbind is what I am trying to do.  I just
don't know how to do it for every component (2 in this case) of the list. 
I've been able to work with R to apply a function across all components when
there is just one list but I am having trouble working with multiple lists
at the same time.  

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This should give you what you want and it is simpler than the earlier
version:

a1<-  array(1:6, dim=c(2,3))
a2<-  array(7:12, dim=c(2,3))
l1<-  list(a1,a2)

a3<-  array(1:4, dim=c(2,2))
a4<-  array(5:8, dim=c(2,2))
l2<-  list(a3,a4)

pattern <- cbind(c(1, 2, 2, 3), c(1, 1, 2, 2))
lnew <- lapply(1:length(l1), function(i) 
  (l1[[i]][,pattern[,1]]+l2[[i]][,pattern[,2]])/2)
lnew

If all the information from your several posts had been included in the
original request, we could have responded more quickly. 

----------------------------------------------
David L Carlson
Associate Professor of Anthropology
Texas A&M University
College Station, TX 77843-4352

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of Hans Thompson
> Sent: Thursday, May 24, 2012 5:19 PM
> To: r-help at r-project.org
> Subject: Re: [R] applying cbind (or any function) across all components
> in a list
> 
> Yes. This gives me:
> 
>      [,1] [,2] [,3] [,4]
> [1,]    1    2    3    4
> [2,]    2    3    4    5
>      [,1] [,2] [,3] [,4]
> [1,]    6    7    8    9
> [2,]    7    8    9   10
> 
> BUT, how can I have it still within components like
> 
> [[1]]
>      [,1] [,2] [,3] [,4]
> [1,]    1    2    3    4
> [2,]    2    3    4    5
> 
> [[2]]
>      [,1] [,2] [,3] [,4]
> [1,]    6    7    8    9
> [2,]    7    8    9   10
> 
> How should I have phrased my question to be specific to this result?
> 
> Thanks.
> 
> --
> View this message in context: http://r.789695.n4.nabble.com/applying-
> cbind-or-any-function-across-all-components-in-a-list-
> tp4631128p4631258.html
> Sent from the R help mailing list archive at Nabble.com.
> 
> ______________________________________________
> R-help at 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.

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?
>
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context:http://r.789695.n4.nabble.com/applying-cbind-or-any-function-across-all-components-in-a-list-tp4631128p4631260.html
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