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? Thanks Karim Ô__ c/ /'_;~~~~kmezhoud (*) \(*) ⴽⴰⵔⵉⵎ ⵎⴻⵣⵀⵓⴷ http://bioinformatics.tn/ On Mon, Jan 19, 2015 at 4:36 PM, Ben Tupper <ben.bigh...@gmail.com> wrote: > Hi, > > On Jan 18, 2015, at 4:36 PM, Karim Mezhoud <kmezh...@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@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. > > [[alternative HTML version deleted]] ______________________________________________ R-help@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.
