ICAMS (version 2.0.7)

as.catalog: Create a catalog from a numeric matrix or numeric data.frame.

Description

Create a catalog from a numeric matrix or numeric data.frame.

Usage

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

Arguments

object

A numeric matrix or numeric data.frame. This object 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.

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.

Value

A catalog as described in ICAMS.

Examples

# NOT RUN {
# Create an SBS96 catalog of human GRCh37 from genome region with all 
# mutation counts equal to 1.  
object <- matrix(1, nrow = 96, ncol = 1, 
                 dimnames = list(catalog.row.order$SBS96))
catSBS96 <- as.catalog(object, ref.genome = "hg19", region = "genome")
# }