sig_operation: Obtain or Modify Signature Information

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Obtain or Modify Signature Information

Description

Obtain or Modify Signature Information

Usage

sig_names(sig)

sig_modify_names(sig, new_names)

sig_number(sig)

sig_attrs(sig)

sig_signature(sig, normalize = c("row", "column", "raw", "feature"))

sig_exposure(sig, type = c("absolute", "relative"))

Arguments

sig	a Signature object obtained either from sig_extract or sig_auto_extract.
new_names	new signature names.
normalize	one of 'row', 'column', 'raw' and "feature", for row normalization (signature), column normalization (component), raw data, row normalization by feature, respectively.
type	one of 'absolute' and 'relative'.

Value

a Signature object or data.

Examples

## Operate signature names
load(system.file("extdata", "toy_mutational_signature.RData",
  package = "sigminer", mustWork = TRUE
))
sig_names(sig2)
cc <- sig_modify_names(sig2, new_names = c("Sig2", "Sig1", "Sig3"))
sig_names(cc)

# The older names are stored in tags.
print(attr(cc, "tag"))
## Get signature number
sig_number(sig2)
## Get signature attributes
sig_number(sig2)
## Get signature matrix
z <- sig_signature(sig2)
z <- sig_signature(sig2, normalize = "raw")
## Get exposure matrix
## Of note, this is different from get_sig_exposure()
## it returns a matrix instead of data table.
z <- sig_exposure(sig2) # it is same as sig$Exposure
z <- sig_exposure(sig2, type = "relative") # it is same as sig2$Exposure.norm

sigminer documentation built on Aug. 21, 2023, 9:08 a.m.