as.catalog {ICAMS}

Create a catalog from a matrix, data.frame, or vector

Description

Create a catalog from a matrix, data.frame, or vector

Usage

as.catalog(
  object,
  ref.genome = NULL,
  region = "unknown",
  catalog.type = "counts",
  abundance = NULL,
  infer.rownames = FALSE
)

Arguments

object

A numeric matrix, numeric data.frame, or vector. If a vector, converted to a 1-column matrix with rownames taken from the element names of the vector and with column name "Unknown". If argument infer.rownames is FALSE then this argument must have rownames to denote the mutation types. See CatalogRowOrder for more details.

ref.genome

A ref.genome argument as described in ICAMS.

region

A character string designating a region, one of genome, transcript, exome, unknown; see ICAMS. If the catalog type is a stranded catalog type (SBS192 or DBS144), region = "genome" will be silently converted to "transcript".

catalog.type

One of "counts", "density", "counts.signature", "density.signature".

abundance

If NULL, then inferred if ref.genome is one of the reference genomes known to ICAMS and region is not unknown. See ICAMS. The argument abundance should contain the counts of different source sequences for mutations in the same format as the numeric vectors in all.abundance.

infer.rownames

If TRUE, and object has no rownames, then assume the rows of object are in the correct order and add the rownames implied by the number of rows in object (e.g. rownames for SBS 192 if there are 192 rows). If TRUE, be sure the order of rows is correct.

Value

A catalog as described in ICAMS.

Examples

# Create an SBS96 catalog with all mutation counts equal to 1.  
object <- matrix(1, nrow = 96, ncol = 1, 
                 dimnames = list(catalog.row.order$SBS96))
catSBS96 <- as.catalog(object)