dgCMatToJMat {scellpam}

dgCMatToJMat

Description

Gets a dgCMatrix object (sparse matrix of the 'Matrix' package) and writes to a disk file the binary matrix of counts contained in it in the jmatrix binary format. Plase, see Details below to know more about the extraction of the sparse matrices from Seurat or similar single cell formats.

Usage

dgCMatToJMat(
  q,
  fname,
  mtype = "sparse",
  ctype = "raw",
  valuetype = "float",
  transpose = FALSE,
  comment = ""
)

Arguments

q

The dgCMatrix object

fname

A string with the name of the binary output file

mtype

A string to indicate the matrix type: 'full' or 'sparse'. Default: 'sparse'

ctype

The string 'raw' or 'log1' to write raw counts or log(counts+1), or the normalized versions, 'rawn' and 'log1n', which normalize ALWAYS BY COLUMNS (before transposition, if requested to transpose). Default: raw

valuetype

The data type to store the matrix. It must be one of the strings 'uint32', 'float' or 'double'. Default: float

transpose

Boolean to indicate if the matrix should be transposed before writing. See Details for a comment about this. Default: FALSE

comment

A comment to be stored with the matrix. Default: "" (no comment)

Details

We have found that, in some Seurat objects, the dgCMatrix to be passed to this function can be extracted as q@assays$RNA@counts, being q the Seurat S4 object.
In other cases this matrix is obtained as [e-mail].
In any case, we assume that this matrix has slots Dimnames (with a list of strings in Dimnames[[0]] as rownames and Dimnames[[1]] as column names) as long as slots with names i, p and x as described in the documentation of the 'Matrix' package on sparse matrices.

The parameter transpose has the default value of FALSE. But don't forget to set it to TRUE if you want the cells (which in single cell common practice are by columns) to be written by rows. This will be needed later to calculate the dissimilarity matrix, if this is the next step of your workflow. See help of CalcAndWriteDissimilarityMatrix

Value

No return value, called for side effects (creates a file)

Examples

# Sorry, we cannot provide an example here, since it would need the load of the Seurat package.
# Please, see the vignette for examples