[R] Cube of Matrices or list of Matrices

[Ben Tupper]

Hi again,

On Jan 19, 2015, at 1:53 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote:

> Yes Many thanks.
> That is my request using lapply.
> 
> do.call(cbind,col1)
> 
>  converts col1 to matrix but does not fill empty value with NA.
> 
> Even for
> 
> matrix(unlist(col1), ncol=5,byrow = FALSE)
> 
> 
> How can get Matrix class of col1? And fill empty values with NA?
> 

Perhaps best is to determine the maximum number of rows required first, then force each subset to have that length.

# make a list of matrices, each with nCol columns and differing
# number of rows
nCol <- 3
nRow <- sample(3:10, 5)
x <- lapply(nRow, function(x, nc) {matrix(x:(x + nc*x - 1), ncol = nc, nrow = x)}, nCol)
x

# make a simple function to get a single column from a matrix
getColumn <- function(x, colNum, len = nrow(x)) {
   y <- x[,colNum]
   length(y) <- len
   y
}

# what is the maximum number of rows
n <- max(sapply(x, nrow))

# use the function to get the column from each matrix
col1 <- lapply(x, getColumn, 1, len = n)
col1

do.call(cbind, col1)
      [,1] [,2] [,3] [,4] [,5]
 [1,]    3    8    5    7    9
 [2,]    4    9    6    8   10
 [3,]    5   10    7    9   11
 [4,]   NA   11    8   10   12
 [5,]   NA   12    9   11   13
 [6,]   NA   13   NA   12   14
 [7,]   NA   14   NA   13   15
 [8,]   NA   15   NA   NA   16
 [9,]   NA   NA   NA   NA   17

Ben

> Thanks
> Karim
> 
> 
>   Ô__
>  c/ /'_;~~~~kmezhoud
> (*) \(*)   ⴽⴰⵔⵉⵎ  ⵎⴻⵣⵀⵓⴷ
> http://bioinformatics.tn/
> 
> 
> 
> On Mon, Jan 19, 2015 at 4:36 PM, Ben Tupper <ben.bighair at gmail.com> wrote:
> Hi,
> 
> On Jan 18, 2015, at 4:36 PM, Karim Mezhoud <kmezhoud at gmail.com> wrote:
> 
> > Dear All,
> > I am trying to get correlation between  Diseases (80) in columns and
> > samples in rows (UNEQUAL) using gene expression (at less 1000,numeric). For
> > this I can use CORREP package with cor.unbalanced function.
> >
> > But before to get this final matrix I need to load and to store the
> > expression of 1000 genes for every Disease (80). Every disease has
> > different number of samples (between 50 - 500).
> >
> > It is possible to get a cube of matrices with equal columns but unequal
> > rows? I think NO and I can't use array function.
> >
> > I am trying to get à list of matrices having the same number of columns but
> > different number of rows. as
> >
> > Cubist <- vector("list", 1)
> > Cubist$Expression <- vector("list", 1)
> >
> >
> > for (i in 1:80){
> >
> > matrix <- function(getGeneExpression[i])
> > Cubist$Expression[[Disease[i]]] <- matrix
> >
> > }
> >
> > At this step I have:
> > length(Cubist$Expression)
> > #80
> > dim(Cubist$Expression$Disease1)
> > #526 1000
> > dim(Cubist$Expression$Disease2)
> > #106  1000
> >
> > names(Cubist$Expression$Disease1[4])
> > #ABD
> >
> > names(Cubist$Expression$Disease2[4])
> > #ABD
> >
> > Now I need to built the final matrices for every genes (1000) that I will
> > use for CORREP function.
> >
> > Is there a way to extract directly the first column (first gene) for all
> > Diseases (80)  from Cubist$Expression? or
> >
> 
> I don't understand most your question, but the above seems to be straight forward.  Here's a toy example:
> 
> # make a list of matrices, each with nCol columns and differing
> # number of rows, nRow
> nCol <- 3
> nRow <- sample(3:10, 5)
> x <- lapply(nRow, function(x, nc) {matrix(x:(x + nc*x - 1), ncol = nc, nrow = x)}, nCol)
> x
> 
> # make a simple function to get a single column from a matrix
> getColumn <- function(x, colNum) {
>    return(x[,colNum])
> }
> 
> # use the function to get the column from each matrix
> col1 <- lapply(x, getColumn, 1)
> col1
> 
> Does that help answer this part of your question?  If not, you may need to create a very small example of your data and post it here using the head() and dput() functions.
> 
> Ben
> 
> 
> 
> > I need to built 1000 matrices with 80 columns and unequal rows?
> >
> > Cublist$Diseases <- vector("list", 1)
> >
> > for (k in 1:1000){
> > for (i in 1:80){
> >
> > Cublist$Diseases[[gene[k] ]] <- Cubist$Expression[[Diseases[i] ]][k]
> > }
> >
> > }
> >
> > This double loops is time consuming...Is there a way to do this faster?
> >
> > Thanks,
> > karim
> >  Ô__
> > c/ /'_;~~~~kmezhoud
> > (*) \(*)   ⴽⴰⵔⵉⵎ  ⵎⴻⵣⵀⵓⴷ
> > http://bioinformatics.tn/
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
> 
> 

Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544
http://www.bigelow.org









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