seaMass_delta-class: seaMass-delta
In biospi/deamass: Statistical modelling for mass spectrometry omics

seaMass_delta-class

R Documentation

seaMass-delta

Description

Perform seaMass-delta differential expression analysis and false discovery rate correction on normalised group-level quants output by seaMass-theta

Usage

seaMass_delta(
  fit,
  data.design = assay_design(fit),
  name = "default",
  control = delta_control(),
  ...
)

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

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

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

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

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

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

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

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

## S4 method for signature 'seaMass_delta'
group_quants_de(
  object,
  groups = NULL,
  summary = TRUE,
  type = "group.quants.de",
  chains = 1:control(object)@nchain,
  as.data.table = FALSE
)

## S4 method for signature 'seaMass_delta'
component_deviations_de(
  object,
  components = NULL,
  summary = TRUE,
  type = "component.deviations.de",
  chains = 1:control(object)@nchain,
  as.data.table = FALSE
)

## S4 method for signature 'seaMass_delta'
group_quants_fdr(
  object,
  groups = NULL,
  summary = TRUE,
  type = "group.quants.fdr",
  chains = 1:control(object)@nchain,
  as.data.table = FALSE
)

## S4 method for signature 'seaMass_delta'
component_deviations_fdr(
  object,
  groups = NULL,
  summary = TRUE,
  type = "component.deviations.fdr",
  chains = 1:control(object)@nchain,
  as.data.table = FALSE
)

add_seaMass_spikein_truth(data.fdr)

add_Navarro_spikein_truth(data.fdr)

## S4 method for signature 'sigma_block'
group_means(
  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-Σ.
`data.design`	Optionally, a data.frame created by new_design and then customised, which specifies sample names, RefWeight channels, and any covariates specified by the experimental design.
`name`	Name of folder on disk where all intermediate and output data will be stored; default is `"output"`.
`control`	A control object created with new_delta_control specifying control parameters for the differential analysis.

Value

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

Functions

seaMass_delta: Runs seaMass-Σ.
open_delta: Open a complete seaMass_delta run from the supplied seaMass_sigma fir object and name.
run,seaMass_delta-method: Run.
name,seaMass_delta-method: Get name.
filepath,seaMass_delta-method: Get path.
parent,seaMass_delta-method: Get the seaMass_sigma object.
control,seaMass_delta-method: Get the fit_control.
assay_design,seaMass_delta-method: Get the study design as a data.frame.
del,seaMass_delta-method: Delete the seaMass_delta run from disk.
group_quants_de,seaMass_delta-method: Get the model differential expression as a data.frame.
component_deviations_de,seaMass_delta-method: Get the component deviations differential expression as a data.frame.
group_quants_fdr,seaMass_delta-method: Get the model differential expression as a data.frame.
component_deviations_fdr,seaMass_delta-method: Get the component deviations differential expression as a data.frame.
add_seaMass_spikein_truth: Add our spikein ground truth to the object of group_fdr pr component_deviations_fdr.
add_Navarro_spikein_truth: Add Navarro spikein ground truth to the object of group_fdr pr component_deviations_fdr.
group_means,sigma_block-method: Get the model group means as a data.frame.