methods {signeR} | R Documentation |
setSamples: Define sample names for a SignExp object, according to the
"names" argument.
setMutations: Define mutation names for a SignExp object, according to the
"mutations" argument.
Normalize: Normalize a SignExp object so that the entries of each
signature sum up to one.
Reorder_signatures: Change the order of the signatures in a SignExp object.
New signature order wil be defined by the "ord" argument.
Reorder_samples: Change samples order, according to ord parameter.
Reorder_mutations: Change mutations order, according to ord parameter.
Average_sign: Exports an aproximation of the signatures obtained by the
averages of the samples for the signature matrix P.
Median_sign: Exports an aproximation of the signatures obtained by the
medians of the samples for signature matrix P.
Average_exp: Exports an aproximation of the exposures obtained by the
averages of the samples for exposure matrix E.
Median_exp: Exports an aproximation of the exposures obtained by the medians of the samples for exposure matrix E.
## S4 method for signature 'SignExp' setSamples(signexp_obj, names) ## S4 method for signature 'SignExp' setMutations(signexp_obj, mutations) ## S4 method for signature 'SignExp' Normalize(signexp_obj) ## S4 method for signature 'SignExp,numeric' Reorder_signatures(signexp_obj, ord) ## S4 method for signature 'SignExp,numeric' Reorder_samples(signexp_obj, ord) ## S4 method for signature 'SignExp,numeric' Reorder_mutations(signexp_obj, ord) ## S4 method for signature 'SignExp' Average_sign(signexp_obj, normalize=TRUE) ## S4 method for signature 'SignExp' Median_sign(signexp_obj, normalize=TRUE) ## S4 method for signature 'SignExp' Average_exp(signexp_obj, normalize=TRUE) ## S4 method for signature 'SignExp' Median_exp(signexp_obj, normalize=TRUE)
signexp_obj |
a SignExp object returned by signeR function. e.g.: sig$SignExposures |
names |
Vector of sample names. |
mutations |
Vector of mutations, e.g. "C>A:TCG". |
normalize |
Whether the signatures should be normalized before extracting approximations. Default is TRUE. |
ord |
Vector with the new signature order. |
setSamples, setMutations, Normalize and Reorder_*
returns a modified SignExp object.
Average_sign, Median_sign, Average_exp and Median_exp return a
matrix with the corresponding approximation.
# each function needs the SignExposures object # which is part of the result of the signeR() call signexp <- Normalize(signatures$SignExposures) signexp <- Reorder_signatures(signatures$SignExposures,ord=c(2,1)) matrix_p <- Median_sign(signatures$SignExposures) # etc ... # see also vignette(package="signeR")