Obtain or Modify Signature Information

Obtain or Modify Signature Information

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)
#> [1] "Sig1" "Sig2" "Sig3"
cc <- sig_modify_names(sig2, new_names = c("Sig2", "Sig1", "Sig3"))
sig_names(cc)
#> [1] "Sig2" "Sig1" "Sig3"

# The older names are stored in tags.
print(attr(cc, "tag"))
#> [1] "Older names:Sig1,Sig2,Sig3;"
## Get signature number
sig_number(sig2)
#> [1] 3
## Get signature attributes
sig_number(sig2)
#> [1] 3
## 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