DEqMS contrast analysis facade
DEqMS contrast analysis facade
Details
Encapsulates the pipeline: strategy_lm ->
build_model -> Contrasts ->
merge with ContrastsMissing ->
ContrastsModeratedDEqMS.
See also
Other modelling:
Contrasts,
ContrastsFirth,
ContrastsLMFacade,
ContrastsLMMissingFacade,
ContrastsLimma,
ContrastsLimmaFacade,
ContrastsLmerFacade,
ContrastsMissing,
ContrastsModerated,
ContrastsModeratedDEqMS,
ContrastsPlotter,
ContrastsProDA,
ContrastsROPECA,
ContrastsROPECAFacade,
ContrastsTable,
INTERNAL_FUNCTIONS_BY_FAMILY,
LR_test(),
Model,
ModelFirth,
ModelLimma,
build_contrast_analysis(),
build_model(),
build_model_limma(),
build_model_logistf(),
contrasts_fisher_exact(),
get_anova_df(),
get_complete_model_fit(),
get_p_values_pbeta(),
group_label(),
isSingular_lm(),
linfct_all_possible_contrasts(),
linfct_factors_contrasts(),
linfct_from_model(),
linfct_matrix_contrasts(),
merge_contrasts_results(),
model_analyse(),
model_summary(),
moderated_p_deqms(),
moderated_p_deqms_long(),
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_build_models_logistf(),
sim_make_model_lm(),
sim_make_model_lmer(),
strategy_limma(),
strategy_logistf(),
summary_ROPECA_median_p.scaled()
Methods
Method new()
initialize
Usage
ContrastsDEqMSFacade$new(lfqdata, modelstr, contrasts, ...)Arguments
lfqdataLFQData object
modelstrmodel formula string (e.g. "~ group_")
contrastsnamed character vector of contrasts
...passed to
strategy_lm
Examples
istar <- sim_lfq_data_protein_config(Nprot = 50)
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
lfqdata <- LFQData$new(istar$data, istar$config)
lfqdata$rename_response("transformedIntensity")
contrasts <- c("A_vs_Ctrl" = "group_A - group_Ctrl")
fa <- ContrastsDEqMSFacade$new(lfqdata, "~ group_", contrasts)
#> Joining with `by = join_by(protein_Id)`
head(fa$get_contrasts())
#> determine linear functions:
#> Warning: linfct_matrix_contrasts: computed 0/2 contrasts; failed 2: A_vs_Ctrl, avg_A_vs_Ctrl. ℹ In argument: `A_vs_Ctrl = group_A - group_Ctrl`.
#> Caused by error:
#> ! object 'group_A' not found; ℹ In argument: `avg_A_vs_Ctrl = (group_A + group_Ctrl)/2`.
#> Caused by error:
#> ! object 'group_A' not found
#> get_contrasts -> contrasts_linfct
#> contrasts_linfct
#> Joining with `by = join_by(protein_Id, contrast)`
#> Warning: moderated_p_deqms_long: warnings in 1/1 groups. contrast=A_vs_Ctrl (pseudoinverse used at 1; neighborhood radius 1; reciprocal condition number 2.362e-17)
#> # A tibble: 6 × 14
#> facade contrast modelName protein_Id diff std.error avgAbd statistic df
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <int>
#> 1 deqms A_vs_Ctrl WaldTest_… 0EfVhX~71… 3.00 0.886 18.8 4.77 6
#> 2 deqms A_vs_Ctrl WaldTest_… 0m5WN4~35… 0.222 0.912 20.4 0.342 8
#> 3 deqms A_vs_Ctrl WaldTest_… 76k03k~97… 0.509 0.464 19.9 0.825 9
#> 4 deqms A_vs_Ctrl WaldTest_… 7QuTub~55… -1.22 0.874 23.4 -1.57 8
#> 5 deqms A_vs_Ctrl WaldTest_… 7cbcrd~04… 1.38 0.690 16.5 1.35 3
#> 6 deqms A_vs_Ctrl WaldTest_… 7soopj~34… 0.822 0.617 25.9 1.13 9
#> # ℹ 5 more variables: p.value <dbl>, conf.low <dbl>, conf.high <dbl>,
#> # sigma <dbl>, FDR <dbl>
fa$to_wide()
#> Warning: moderated_p_deqms_long: warnings in 1/1 groups. contrast=A_vs_Ctrl (pseudoinverse used at 1; neighborhood radius 1; reciprocal condition number 2.362e-17)
#> # A tibble: 49 × 5
#> protein_Id diff.A_vs_Ctrl p.value.A_vs_Ctrl FDR.A_vs_Ctrl statistic.A_vs_Ctrl
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 0EfVhX~71… 3.00 0.00310 0.152 4.77
#> 2 0m5WN4~35… 0.222 0.741 0.816 0.342
#> 3 76k03k~97… 0.509 0.431 0.816 0.825
#> 4 7QuTub~55… -1.22 0.154 0.584 -1.57
#> 5 7cbcrd~04… 1.38 0.271 0.705 1.35
#> 6 7soopj~34… 0.822 0.288 0.705 1.13
#> 7 9VUkAq~86… -1.95 0.0232 0.228 -2.80
#> 8 At886V~03… -0.290 0.806 0.823 -0.279
#> 9 BEJI92~54… 0.961 0.232 0.669 1.31
#> 10 CGzoYe~12… -2.10 0.00867 0.175 -3.34
#> # ℹ 39 more rows