seaMass_sigma-class: seaMass-Σ
In biospi/deamass: Statistical modelling for mass spectrometry omics

seaMass_sigma-class

R Documentation

seaMass-Σ

Description

Fits the seaMass-Σ Bayesian group-level quantification model to imported data.

Usage

seaMass_sigma(
  data,
  data.design = new_assay_design(data),
  path = "fit",
  user = Sys.info()[["user"]],
  run = TRUE,
  control = sigma_control(),
  ...
)

open_sigma(path = "fit.seaMass", quiet = FALSE, force = FALSE)

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

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

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

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

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

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

## S4 method for signature 'seaMass_sigma'
groups(object, summary = FALSE, as.data.table = FALSE)

## S4 method for signature 'seaMass_sigma'
top_groups(object, n = 512)

## S4 method for signature 'seaMass_sigma'
components(object, summary = FALSE, as.data.table = FALSE)

## S4 method for signature 'seaMass_sigma'
assay_groups(object, summary = FALSE, as.data.table = FALSE)

## S4 method for signature 'seaMass_sigma'
assay_components(object, summary = FALSE, as.data.table = FALSE)

## S4 method for signature 'seaMass_sigma'
measurements(object, summary = FALSE, as.data.table = FALSE)

## S4 method for signature 'seaMass_sigma'
blocks(object)

## S4 method for signature 'seaMass_sigma'
open_thetas(object, quiet = FALSE, force = FALSE)

## S4 method for signature 'seaMass_sigma'
open_deltas(object, quiet = FALSE, force = FALSE)

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

## S4 method for signature 'seaMass_sigma'
timings(object, input = "model1", as.data.table = FALSE)

## S4 method for signature 'seaMass_sigma'
priors(object, input = "model1", as.data.table = FALSE)

## S4 method for signature 'seaMass_sigma'
assay_stdevs(object, input = "model1", as.data.table = FALSE)

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

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

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

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

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

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

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

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

Arguments

`data`	A data.frame of input data as returned by import_MaxQuant, import_OpenSWATH, import_ProteinPilot or import_ProteomeDiscoverer, .
`data.design`	A data.frame created by new_assay_design and then customised, which specifies assay names and block design.
`path`	Name of folder prefix on disk where all intermediate and output data will be stored.
`run`	Run seaMass-Σ now, or just prepare it for later execution on e.g. a HPC cluster?
`control`	A control object created with sigma_control specifying control parameters for the model.

Value

A seaMass_sigma object, which allows access to metadata and each block's sigma_block object to access various results.

Functions

seaMass_sigma: Runs seaMass-Σ.
open_sigma: Open a complete seaMass_sigma run from the supplied path.
del,seaMass_sigma-method: Delete the seaMass_sigma run from disk.
root,seaMass_sigma-method: Get the seaMass_sigma object.
name,seaMass_sigma-method: Get name.
filepath,seaMass_sigma-method: Get path.
run,seaMass_sigma-method: Run.
control,seaMass_sigma-method: Get the sigma_control.
groups,seaMass_sigma-method: Get the groups as a data.frame.
top_groups,seaMass_sigma-method: Get the n groups with the most quantified components that are present in all blocks data.frame.
components,seaMass_sigma-method: Get the groups as a data.frame.
assay_groups,seaMass_sigma-method: Get the assay groups as a data.frame.
assay_components,seaMass_sigma-method: Get the assay groups as a data.frame.
measurements,seaMass_sigma-method: Get the groups as a data.frame.
blocks,seaMass_sigma-method: Get the list of sigma_block objects for the blocks.
open_thetas,seaMass_sigma-method: Open the list of seaMass_delta objects.
open_deltas,seaMass_sigma-method: Open the list of seaMass_delta objects.
assay_design,seaMass_sigma-method: Get the study design as a data.frame.
timings,seaMass_sigma-method: Get the model timings as a data.frame.
priors,seaMass_sigma-method: Get priors as a data.frame.
assay_stdevs,seaMass_sigma-method: Get the model assay stdevs as a data.frame.
assay_deviations,seaMass_sigma-method: Get the model assay deviations as a data.frame.
measurement_means,seaMass_sigma-method: Get the model measurement means as a data.frame.
measurement_stdevs,seaMass_sigma-method: Get the model measurement stdevs as a data.frame.
component_means,seaMass_sigma-method: Get the model component means as a data.frame.
component_stdevs,seaMass_sigma-method: Get the model component stdevs as a data.frame.
component_deviations,seaMass_sigma-method: Gets the model component deviations as a data.frame.
group_quants,seaMass_sigma-method: Get the model group quantifications as a data.frame.
group_means,seaMass_sigma-method: Get the model group means as a data.frame.