sigma_block-class: seaMass-Σ block

In biospi/deamass: Statistical modelling for mass spectrometry omics

seaMass-Σ block

Description

The results of a seaMass-Σ block to a single block, returned by /linkseaMass_sigma /codeblocks() function

Usage

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

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

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

## S4 method for signature 'sigma_block'
container(object)

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

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

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

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

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

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

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

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

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

## S4 method for signature 'sigma_block'
summary(object, group, chain, input = "model1")

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

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

## S4 method for signature 'sigma_block'
assay_deviations(
  object,
  assays = NULL,
  summary = TRUE,
  input = "model0",
  chains = 1:control(object)@nchain,
  as.data.table = FALSE
)

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

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

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

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

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

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

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

Methods (by generic)

• filepath: Get the path.

• name: Get the block name.

• root: Get the seaMass_sigma object.

• container: Get the seaMass_sigma object for this block.

• control: Get the sigma_control object for this block.

• blocks: Get the list of sigma_block objects for the blocks.

• groups: Get the group metadata as a data.frame.

• measurements: Get the measurement metadata as a data.frame.

• components: Get the component metadata as a data.frame.

• assay_groups: Get the assay groups as a data.frame.

• assay_components: Get the assay groups as a data.frame.

• assay_design: Get the study design for this block as a data.frame.

• priors: Get the priors if computed.

• summary: Print the model summary for a group.

• timings: Get the model timings as a data.frame.

• assay_stdevs: Get the model assay stdevs as a data.frame.

• assay_deviations: Get the model assay deviations as a data.frame.

• measurement_means: Get the model measurement means as a data.frame.

• measurement_stdevs: Get the model measurement stdevs as a data.frame.

• component_means: Get the model component means as a data.frame.

• component_stdevs: Get the model component stdevs as a data.frame.

• component_deviations: Gets the model component deviations as a data.frame.

• group_quants: Get the model group quantifications as a data.frame.

• blocks: Get the list of theta_block objects for the blocks.

biospi/deamass documentation built on May 20, 2023, 3:30 a.m.