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"))
sig | a |
---|---|
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'. |
a Signature
object or data.
## 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