SAINTexpress contrast analysis facade

SAINTexpress contrast analysis facade

SAINTexpress contrast analysis facade

Value

An R6 class generator.

Details

Encapsulates the SAINTexpress pipeline so that it can be reached through the same facade-registry dispatch as the prolfqua built-in methods (lm, limma, firth, ...). Wraps protein_2localSaint -> runSaint -> ContrastsSAINTexpress, with bait / control / gene / protein-length columns resolved from the annotation data attached to the input LFQData.

Differs from LM-style facades in three ways:

• The contrast set is derived from the bait column (one bait vs. controls), so the contrasts argument is ignored.

• The output schema uses Bait / log2_EFCs / SaintScore / BFDR; p.value is NA.

• The facade carries SAINT input tables and the raw SAINTexpress result via extra_artifacts() for downstream report rendering.

See also

Other modelling: ContrastsSAINTexpress

Super class

prolfqua::ContrastsInterface -> ContrastsSAINTFacade

Public fields

contrast

wrapped ContrastsSAINTexpress object

saint_input

SAINTexpress input tables (inter/prey/bait)

saint_result

raw SAINTexpress result list

protein_id

hierarchy key the SAINT Prey column is mapped back to

.lfqdata

stored reference to input LFQData

.row_annot

stored reference to row annotation

Methods

Public methods

• ContrastsSAINTFacade$new()

• ContrastsSAINTFacade$get_contrasts()

• ContrastsSAINTFacade$get_Plotter()

• ContrastsSAINTFacade$to_wide()

• ContrastsSAINTFacade$get_missing()

• ContrastsSAINTFacade$get_ora()

• ContrastsSAINTFacade$get_rank()

• ContrastsSAINTFacade$extra_artifacts()

• ContrastsSAINTFacade$clone()

Inherited methods

• prolfqua::ContrastsInterface$column_description()
• prolfqua::ContrastsInterface$contrast_summary_table()
• prolfqua::ContrastsInterface$filter_significant()
• prolfqua::ContrastsInterface$get_config()
• prolfqua::ContrastsInterface$get_contrast_sides()

---

Method new()

initialize

Usage

ContrastsSAINTFacade$new(
  lfqdata,
  modelstr = NULL,
  contrasts = NULL,
  row_annot = NULL,
  spc = FALSE,
  engine = "r"
)

Arguments

lfqdata

aggregated LFQData object with bait / control columns in the annotation

modelstr

ignored — SAINT derives contrasts from the bait column; accepted for facade uniformity

contrasts

ignored for the same reason

row_annot

data.frame with protein-level annotation (must contain the hierarchy key column). When NULL, falls back to lfqdata$hierarchy_keys() content from the long table.

spc

if TRUE run SAINTexpress-spc; default FALSE (intensity model).

engine

SAINTexpress engine; one of "r" (default) or whatever runSaint accepts.

---

Method get_contrasts()

get contrast results from the wrapped ContrastsSAINTexpress; adds a facade column matching the lm/limma facade convention.

Usage

ContrastsSAINTFacade$get_contrasts(...)

Arguments

...

passed to ContrastsSAINTexpress$get_contrasts

---

Method get_Plotter()

plotter for SAINT contrasts (delegates)

Usage

ContrastsSAINTFacade$get_Plotter(...)

Arguments

...

passed to ContrastsSAINTexpress$get_Plotter

---

Method to_wide()

wide format (delegates)

Usage

ContrastsSAINTFacade$to_wide(...)

Arguments

...

passed to ContrastsSAINTexpress$to_wide

---

Method get_missing()

protein × bait pairs absent from SAINT output

Usage

ContrastsSAINTFacade$get_missing()

Returns

data.frame with hierarchy and bait columns

---

Method get_ora()

ORA input table (delegates)

Usage

ContrastsSAINTFacade$get_ora(
  up = TRUE,
  FDR_threshold = 0.05,
  diff_threshold = 1
)

Arguments

up

if TRUE return bait-enriched prey

FDR_threshold

BFDR threshold

diff_threshold

log2 EFC threshold

---

Method get_rank()

rank table for enrichment tools (delegates; default score is log2_EFCs because SAINTexpress has no p-value)

Usage

ContrastsSAINTFacade$get_rank(score = "log2_EFCs")

Arguments

score

column to use as rank score

---

Method extra_artifacts()

SAINT-specific artifacts to surface in downstream reports. Returns a named list with the SAINT input tables and the raw result list.

Usage

ContrastsSAINTFacade$extra_artifacts()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ContrastsSAINTFacade$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

ContrastsSAINTFacade
#> <ContrastsSAINTFacade> object generator
#>   Inherits from: <prolfqua::ContrastsInterface>
#>   Public:
#>     contrast: NULL
#>     saint_input: NULL
#>     saint_result: NULL
#>     protein_id: 
#>     .lfqdata: NULL
#>     .row_annot: NULL
#>     initialize: function (lfqdata, modelstr = NULL, contrasts = NULL, row_annot = NULL, 
#>     get_contrasts: function (...) 
#>     get_Plotter: function (...) 
#>     to_wide: function (...) 
#>     get_missing: function () 
#>     get_ora: function (up = TRUE, FDR_threshold = 0.05, diff_threshold = 1) 
#>     get_rank: function (score = "log2_EFCs") 
#>     extra_artifacts: function () 
#>     clone: function (deep = FALSE) 
#>   Parent env: <environment: namespace:prolfquasaint>
#>   Locked objects: TRUE
#>   Locked class: FALSE
#>   Portable: TRUE