Wrapper to results produced by SAINTexpress

Wrapper to results produced by SAINTexpress

Wrapper to results produced by SAINTexpress

Value

An R6 class generator.

Details

SAINTexpress writes

See also

summary_ROPECA_median_p.scaled

Other modelling: ContrastsSAINTFacade

Super class

prolfqua::ContrastsInterface -> ContrastsSAINTexpress

Public fields

contrast_result

data.frame with the contrast computation results

modelName

model name

subject_id

subject id defualt 'Prey'

Methods

Public methods

• ContrastsSAINTexpress$new()

• ContrastsSAINTexpress$get_contrast_sides()

• ContrastsSAINTexpress$get_linfct()

• ContrastsSAINTexpress$get_contrasts()

• ContrastsSAINTexpress$get_Plotter()

• ContrastsSAINTexpress$to_wide()

• ContrastsSAINTexpress$get_rank()

• ContrastsSAINTexpress$get_ora()

• ContrastsSAINTexpress$clone()

Inherited methods

• prolfqua::ContrastsInterface$column_description()
• prolfqua::ContrastsInterface$contrast_summary_table()
• prolfqua::ContrastsInterface$extra_artifacts()
• prolfqua::ContrastsInterface$filter_significant()
• prolfqua::ContrastsInterface$get_config()
• prolfqua::ContrastsInterface$get_missing()

---

Method new()

initialize

Usage

ContrastsSAINTexpress$new(
  contrastsdf,
  subject_id = "Prey",
  modelName = "ContrastSaint"
)

Arguments

contrastsdf

return value of runSaint

subject_id

default "Prey"

modelName

name of model

---

Method get_contrast_sides()

show contrasts

Usage

ContrastsSAINTexpress$get_contrast_sides()

Returns

data.frame

---

Method get_linfct()

no available for SaintExpress

Usage

ContrastsSAINTexpress$get_linfct()

---

Method get_contrasts()

get contrasts

Usage

ContrastsSAINTexpress$get_contrasts(all = FALSE)

Arguments

all

should all columns be returned (default FALSE)

global

use a global linear function (determined by get_linfct)

---

Method get_Plotter()

get ContrastsPlotter

Usage

ContrastsSAINTexpress$get_Plotter(
  fc_threshold = 1,
  SaintScore = 0.75,
  bfdr_threshold = 0.1
)

Arguments

fc_threshold

fold change threshold to show

SaintScore

SaintScore threshold to show in the heatmap.

bfdr_threshold

BFDR threshold

Returns

ContrastsPlotter

---

Method to_wide()

convert to wide format

Usage

ContrastsSAINTexpress$to_wide(columns = c("SaintScore", "BFDR"))

Arguments

columns

value column default SaintScore, BFDR

Returns

data.frame

---

Method get_rank()

get signed rank-list input table for enrichment tools.

Usage

ContrastsSAINTexpress$get_rank(score = "log2_EFCs")

Arguments

score

column to use as rank score

Returns

data.frame with subject id, contrast, and score columns.

---

Method get_ora()

get SAINT ORA input table.

Usage

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

Arguments

up

if TRUE return bait-enriched prey, otherwise negative effects

FDR_threshold

BFDR threshold

diff_threshold

log2 EFC threshold

Returns

filtered SAINT contrast data.frame for ORA input.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

ContrastsSAINTexpress$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

seout <- prolfqua::prolfqua_data("data_SAINTe_output")
cse <- ContrastsSAINTexpress$new(seout$list)
stopifnot(dim(cse$to_wide()) == c(64,13))
cse$get_contrast_sides()
#>       contrast group_1 group_2
#> 1 b vs Control       b Control
#> 2 c vs Control       c Control
#> 3 d vs Control       d Control
#> 4 e vs Control       e Control
stopifnot(dim(cse$get_contrasts()) == c(236,7))
cse$get_linfct()
#> NULL
pl <- cse$get_Plotter()
stopifnot(c("gg", "ggplot") %in% class(pl$volcano()$FDR))