- 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.