seaMass_theta-class: seaMass-theta
In biospi/deamass: Statistical modelling for mass spectrometry omics

root,seaMass_delta-method

R Documentation

seaMass-theta

Description

Perform seaMass-theta normalisation on raw group-level quants output by seaMass-sigma

Usage

## S4 method for signature 'seaMass_delta'
root(object)

seaMass_theta(
  fit,
  data.design = assay_design(fit),
  norm.groups = top_groups(fit),
  name = "default",
  control = theta_control(),
  ...
)

open_theta(fit, name = "default", quiet = FALSE, force = FALSE)

## S4 method for signature 'seaMass_theta'
run(object)

## S4 method for signature 'seaMass_theta'
name(object)

## S4 method for signature 'seaMass_theta'
root(object)

## S4 method for signature 'seaMass_theta'
filepath(object)

## S4 method for signature 'seaMass_theta'
parent(object)

## S4 method for signature 'seaMass_theta'
del(object)

## S4 method for signature 'seaMass_theta'
control(object)

## S4 method for signature 'seaMass_theta'
assay_design(object, as.data.table = FALSE)

## S4 method for signature 'seaMass_theta'
assay_means(
  object,
  assays = NULL,
  summary = TRUE,
  input = "model1",
  chains = 1:control(object)@nchain,
  as.data.table = FALSE
)

## S4 method for signature 'seaMass_theta'
group_standards(
  object,
  groups = NULL,
  summary = TRUE,
  input = "model1",
  chains = 1:control(object)@nchain,
  as.data.table = FALSE
)

## S4 method for signature 'seaMass_theta'
group_quants(
  object,
  groups = NULL,
  summary = TRUE,
  input = "model1",
  chains = 1:control(object)@nchain,
  as.data.table = FALSE
)

Arguments

`fit`	A seaMass_sigma object as returned by seaMass-sigma.
`data.design`	Optionally, a data.frame created by new_design and then customised, which specifies RefWeight channels.
`name`	Name of subfolder on disk where all intermediate and output data will be stored; default is `"default"`.
`control`	A control object created with new_theta_control specifying control parameters for the normalisation.
`groups`	Groups to normalise on, default is the top 10 that are in every block (instead of all, just for computational considerations).

Value

A seaMass_theta object that can be interrogated for various metadata and results.

Functions

root,seaMass_delta-method: Get the seaMass_sigma object.
seaMass_theta: Runs seaMass-theta.
open_theta: Open a complete seaMass_theta run from the supplied seaMass_sigma fir object and name.
run,seaMass_theta-method: Run.
name,seaMass_theta-method: Get name.
root,seaMass_theta-method: Get the seaMass_sigma object.
filepath,seaMass_theta-method: Get path.
parent,seaMass_theta-method: Get the seaMass_sigma object.
del,seaMass_theta-method: Delete the seaMass_theta run from disk.
control,seaMass_theta-method: Get the fit_control.
assay_design,seaMass_theta-method: Get the study design as a data.frame.
assay_means,seaMass_theta-method: Get the model assay means as a data.frame.
group_standards,seaMass_theta-method: Get the model group standards as a data.frame.
group_quants,seaMass_theta-method: Get the model group quantifications as a data.frame.