[R] Extract data from Array to Table

[Sven E. Templer]

see inline

On 12 February 2015 at 09:10, Sven E. Templer <sven.templer at gmail.com> wrote:
> Make use of the plyr and reshape2 package (both on CRAN):
>

I forgot:

library(reshape2)

> library(plyr)
> d<-adply(ArrayDiseaseCor, 1:2)
> # adply calls function identity by default
> d<-melt(d)
> d<-subset(d,value>.5)
> head(d)
>
> You will have to rename columns, or adjust arguments in melt/adply.
> Note: use set.seed before sampling for reproducible code!
>
> Best, S.
>
> On 11 February 2015 at 17:11, Karim Mezhoud <kmezhoud at gmail.com> wrote:
>> Dear All,
>> I am facing the task to extract data from array to table. here an example
>> of array.
>>
>> ##Get A list of Matrices with unequal rows
>>
>> Disease <- NULL
>> Diseases <- NULL
>> ListMatByGene <- NULL
>> for(i in 1:3){
>>
>> Disease[[i]] <-matrix(sample(-30:30,25+(5*
>> i)),5+i)
>> rownames(Disease[[i]]) <- paste0("Sample",1:(5+i))
>> colnames(Disease[[i]]) <- paste0("Gene",1:5)
>>
>> D <- paste0("Disease",i)
>> Diseases[[D]] <- Disease[[i]]
>> }
>>
>>
>> ## get the same Column from all matrices
>> getColumn <- function(x, colNum, len = nrow(x)){
>>     y <- x[,colNum]
>>     length(y) <- len
>>     y
>> }
>>
>> ## get Matrices by the same columns of the list of matrices
>> getMatrices <- function(colNums, dataList = x){
>>     # the number of rows required
>>     n <- max(sapply(dataList, nrow))
>>     lapply(colNums, function(x, dat, n) { # iterate along requested columns
>>         do.call(cbind, lapply(dat, getColumn,x, len=n)) # iterate along
>> input data list
>>     }, dataList, n)
>> }
>>
>> ## Rotate the list of matrices by 90°
>> G <- paste0("Gene",1:5)
>> ListMatByGene[G] <- getMatrices(c(1:ncol(Diseases[[1]])),dataList=Diseases)
>>
>> ## get Disease correlation by gene
>> DiseaseCorrelation <- lapply(ListMatByGene,function(x) cor(x,use="na",
>> method="spearman"))
>>
>> ##convert the list of Matrices to array
>> ArrayDiseaseCor <- array(unlist(DiseaseCorrelation), dim =
>> c(nrow(DiseaseCorrelation[[1]]), ncol(DiseaseCorrelation[[1]]),
>> length(DiseaseCorrelation)))
>> dimnames(ArrayDiseaseCor) <- list(names(Diseases), names(Diseases),
>> colnames(Diseases[[1]]))
>>
>> ## Select only correlation bigger than 0.5 from the array
>> FilterDiseaseCor <- apply(ArrayDiseaseCor,MARGIN=c(1,2) ,function(x)
>> x[abs(x)>0.5])
>>
>> ## Final result
>> FilterDiseaseCor
>>
>>          Disease1   Disease2  Disease3
>> Disease1 Numeric,5  Numeric,2 -0.9428571
>> Disease2 Numeric,2  Numeric,5 Numeric,2
>> Disease3 -0.9428571 Numeric,2 Numeric,5
>>
>>
>> Question is:
>> How can get a table as:
>>
>> D1              D2               Cor       Gene
>> Disease1    Disease2      -0.94    Gene2
>> Disease1    Disease2       0.78    Gene4
>> Disease3    Disease2       0.5      Gene5
>> ...
>>
>> and
>>                  Disease1   Disease2      Disease3
>> Disease1        5                1                0
>> Disease2        1                 5                3
>> Disease3        0                  3               5
>>
>> Or in general, How can I extract data from Array to Table?
>>
>> Thanks
>> Karim
>>
>>         [[alternative HTML version deleted]]
>>
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