Estimate contrasts using Wald Test

Estimate contrasts using Wald Test

Estimate contrasts using Wald Test

See also

Other modelling: ContrastsMissing, ContrastsModerated, ContrastsPlotter, ContrastsProDA, ContrastsROPECA, ContrastsTable, INTERNAL_FUNCTIONS_BY_FAMILY, LR_test(), Model, build_model(), contrasts_fisher_exact(), get_anova_df(), get_complete_model_fit(), get_p_values_pbeta(), isSingular_lm(), linfct_all_possible_contrasts(), linfct_factors_contrasts(), linfct_from_model(), linfct_matrix_contrasts(), merge_contrasts_results(), model_analyse(), model_summary(), moderated_p_limma(), moderated_p_limma_long(), my_contest(), my_contrast(), my_contrast_V1(), my_contrast_V2(), my_glht(), pivot_model_contrasts_2_Wide(), plot_lmer_peptide_predictions(), sim_build_models_lm(), sim_build_models_lmer(), sim_make_model_lm(), sim_make_model_lmer(), strategy_lmer(), summary_ROPECA_median_p.scaled()

Super class

prolfqua::ContrastsInterface -> Contrast

Public fields

models

Model

contrasts

character with contrasts

contrastfun

function to compute contrasts

modelName

model name

subject_Id

name of column containing e.g., protein Id's

p.adjust

function to adjust p-values (default prolfqua::adjust_p_values)

contrast_result

data frame containing results of contrast computation

global

use a global linear function (determined by get_linfct)

protein_annot

holds protein annotation

Methods

Public methods

• Contrasts$new()

• Contrasts$get_contrast_sides()

• Contrasts$get_linfct()

• Contrasts$get_contrasts()

• Contrasts$get_Plotter()

• Contrasts$to_wide()

• Contrasts$clone()

Inherited methods

• prolfqua::ContrastsInterface$column_description()

---

Method new()

initialize create Contrast

Usage

Contrasts$new(
  model,
  contrasts,
  p.adjust = prolfqua::adjust_p_values,
  global = FALSE,
  modelName = "WaldTest"
)

Arguments

model

a dataframe with a structure similar to that generated by build_model

contrasts

a character vector with contrast specificiation

p.adjust

function to adjust the p-values

global

development/internal argument (if FALSE determine linfct for each model.)

modelName

name of contrast method, default WaldTest

---

Method get_contrast_sides()

get both sides of contrasts

Usage

Contrasts$get_contrast_sides()

---

Method get_linfct()

get linear functions from contrasts

Usage

Contrasts$get_linfct(global = TRUE, avg = TRUE)

Arguments

global

logical TRUE - get the a linear functions for all models, FALSE - linear function for each model

avg

logical TRUE - get also linfct for averages

---

Method get_contrasts()

get table with contrast estimates

Usage

Contrasts$get_contrasts(all = FALSE)

Arguments

all

should all columns be returned (default FALSE)

Returns

data.frame with contrasts

---

Method get_Plotter()

return ContrastsPlotter creates Contrast_Plotter

Usage

Contrasts$get_Plotter(FCthreshold = 1, FDRthreshold = 0.1)

Arguments

FCthreshold

fold change threshold to show in plots

FDRthreshold

FDR threshold to show in plots

Returns

ContrastsPlotter

---

Method to_wide()

convert to wide format

Usage

Contrasts$to_wide(columns = c("p.value", "FDR", "statistic"))

Arguments

columns

value column default p.value

Returns

data.frame

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Contrasts$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Fitting mixed effects model to peptide data
istar <- prolfqua::sim_lfq_data_peptide_config()
#> creating sampleName from fileName column
#> Warning: no nr_children column specified in the data, adding column nr_children and setting to 1.
#> completing cases

modelFunction <-
strategy_lmer("abundance  ~ group_ + (1 | peptide_Id) + (1 | sample)")

config <- istar$config
config$table$hierarchy_keys_depth()
#> [1] "protein_Id"

mod <- build_model(
 istar$data,
 modelFunction,
 subject_Id = config$table$hierarchy_keys_depth()
 )
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> boundary (singular) fit: see help('isSingular')
#> Warning: There were 4 warnings in `dplyr::mutate()`.
#> The first warning was:
#> ℹ In argument: `linear_model = purrr::map(data, model_strategy$model_fun, pb =
#>   pb)`.
#> ℹ In group 2: `protein_Id = "7cbcrd~5725"`.
#> Caused by warning in `value[[3L]]()`:
#> ! WARN :Error: grouping factors must have > 1 sampled level
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 3 remaining warnings.
#> Joining with `by = join_by(protein_Id)`

ref_lfc <- data.frame(
`(Intercept)` = c(0, 0, 0),
group_B = c(0, 1, 0),
group_Ctrl = c(-1, -1, 1),
row.names = c("groupA_vs_Ctrl", "dil.e_vs_b", "dil.ctrl_vs_b")
)
prolfqua::model_summary(mod)
#> $exists
#> 
#> FALSE  TRUE 
#>     4     6 
#> 
#> $isSingular
#> 
#> FALSE  TRUE 
#>     1     5 
#> 
Contr <- c("groupA_vs_Ctrl" = "group_A - group_Ctrl",
    "dil.e_vs_b" = "group_B - group_Ctrl",
    "dil.ctrl_vs_b" = "group_Ctrl - group_A"
     )
#prolfqua::Contrasts$debug("get_linfct")
#debug(prolfqua:::.linfct)
contrastX <- prolfqua::Contrasts$new(mod, Contr)
y <- contrastX$get_linfct(avg = FALSE)
stopifnot(all(ref_lfc == y))
t <- contrastX$get_linfct(global=FALSE)

x <- contrastX$get_contrasts()
#> determine linear functions:
#> compute contrasts:
#> computing contrasts.
#> Joining with `by = join_by(protein_Id, contrast)`
stopifnot(all(x$p.value < 1 & x$p.value >0))
stopifnot(all(x$avgAbd >0))
stopifnot(all(x$FDR >0 & x$FDR < 1))

x <- contrastX$get_contrast_sides()
xd <- contrastX$column_description()
modelFunction <-
strategy_lm("abundance  ~ group_")
mod <- build_model(
 istar$data,
 modelFunction,
 subject_Id = config$table$hierarchy_keys_depth()
 )
#> Joining with `by = join_by(protein_Id)`
contrastX <- prolfqua::Contrasts$new(mod, Contr)
y <- contrastX$get_linfct(avg = FALSE)
stopifnot(all(ref_lfc == y))