methods: SignExp class methods

In signeR: Empirical Bayesian approach to mutational signature discovery

Description

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.

Usage

## 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)

Arguments

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.

Value

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.

Examples

# 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")

signeR documentation built on Nov. 8, 2020, 8:08 p.m.