MergeExprsMtx function does not exist?

[sushilashenoy]

The tutorial vignette mentions this function by name but the function does not seem to exist.

There is a function called JoinMatrices but this function doesn't do what I'm looking for - my expression matrices are sparse (class dgCMatrix) and this function wants data.frames. I'd prefer not to convert my sparse matrices to data.frames.

[sushilashenoy]

Nevermind, I see now that this function was renamed JoinMatrices so the functionality I am looking for does not exist currently.

[sushilashenoy]

In case anyone else is trying to do this or if you want to add this functionality to the package, here is my quick implementation:

JoinSparseMatrices <- function(x = list()) {
  if (!is.list(x) ) {
    stop("Please specify a list of matrices.")
  } else if ( any(sapply(x, function (y) !canCoerce(y, 'dgCMatrix'))) ) {
    stop("Not all items can be coerced to dgCMatrix.")
  }

  # Use union of genes from each matrix
  all.gene.ids <- sort(Reduce(union, lapply(x, rownames)))

  # Make sure we don't have duplicate cell barcodes
  all.cell.ids <- do.call(c, lapply(x, colnames))
  if ( any(duplicated(all.cell.ids)) ) {
    stop('Duplicate cell IDs found.')
  }

  # Map all matrices to the same rows (all.gene.ids)
  mat.list <- lapply(x, function (mat) {
    mat <- as(mat, 'dgCMatrix')
    mat.sum <- summary(mat) # Get i,j,x format for sparse matrix
    map.genes <- match(rownames(mat), all.gene.ids)
    new.i <- map.genes[mat.sum$i]
    sparseMatrix(i=new.i, j=mat.sum$j, x=mat.sum$x, dims=c(length(all.gene.ids), ncol(mat)), dimnames=list(all.genes, colnames(mat)))
  })

  return ( do.call(cbind, mat.list) )
}

[asenabouth]

Hi @sushilashenoy, Thanks for flagging the error in the vignette - I have fixed it. Great suggestion - I will add some more functionality to the JoinMatrices so it will take and output matrices that are sparse and dense.

[asenabouth]

Extra functionality now added to JoinMatrices.