LM contrast analysis facade
LM contrast analysis facade
Details
Encapsulates the pipeline: strategy_lm ->
build_model -> Contrasts ->
ContrastsModerated.
See also
Other modelling:
Contrasts,
ContrastsDEqMSFacade,
ContrastsFirth,
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
ContrastsLMFacade$new(lfqdata, modelstr, contrasts, ...)Arguments
lfqdataLFQData object
modelstrmodel formula string (e.g. "~ group_")
contrastsnamed character vector of contrasts
...passed to
strategy_lm
Examples
istar <- sim_lfq_data_protein_config()
#> creating sampleName from fileName column
#> completing cases
#> completing cases done
#> setup done
lfqdata <- LFQData$new(istar$data, istar$config)
lfqdata$rename_response("transformedIntensity")
contrasts <- c("A_vs_Ctrl" = "group_A - group_Ctrl")
fa <- ContrastsLMFacade$new(lfqdata, "~ group_", contrasts)
#> Joining with `by = join_by(protein_Id)`
head(fa$get_contrasts())
#> determine linear functions:
#> Warning: linfct_matrix_contrasts: computed 0/2 contrasts; failed 2: A_vs_Ctrl, avg_A_vs_Ctrl. ℹ In argument: `A_vs_Ctrl = group_A - group_Ctrl`.
#> Caused by error:
#> ! object 'group_Ctrl' not found; ℹ In argument: `avg_A_vs_Ctrl = (group_A + group_Ctrl)/2`.
#> Caused by error:
#> ! object 'group_Ctrl' not found
#> get_contrasts -> contrasts_linfct
#> contrasts_linfct
#> Joining with `by = join_by(protein_Id, contrast)`
#> # A tibble: 6 × 14
#> facade modelName protein_Id contrast diff std.error avgAbd statistic df
#> <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 lm WaldTest_… 0EfVhX~00… A_vs_Ct… -2.62 0.660 21.1 -3.51 15.1
#> 2 lm WaldTest_… 7cbcrd~57… A_vs_Ct… 2.80 0.417 20.7 4.06 13.1
#> 3 lm WaldTest_… 9VUkAq~47… A_vs_Ct… 1.67 0.740 20.3 1.97 14.1
#> 4 lm WaldTest_… BEJI92~52… A_vs_Ct… 0.424 0.960 21.0 0.569 15.1
#> 5 lm WaldTest_… CGzoYe~21… A_vs_Ct… -0.598 0.750 30.8 -0.867 16.1
#> 6 lm WaldTest_… Fl4JiV~86… A_vs_Ct… -0.0494 0.603 21.3 -0.0664 15.1
#> # ℹ 5 more variables: p.value <dbl>, conf.low <dbl>, conf.high <dbl>,
#> # sigma <dbl>, FDR <dbl>
fa$to_wide()
#> # A tibble: 9 × 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~0087 -2.62 0.00311 0.0140 -3.51
#> 2 7cbcrd~5725 2.80 0.00132 0.0119 4.06
#> 3 9VUkAq~4703 1.67 0.0684 0.205 1.97
#> 4 BEJI92~5282 0.424 0.578 0.650 0.569
#> 5 CGzoYe~2147 -0.598 0.398 0.598 -0.867
#> 6 Fl4JiV~8625 -0.0494 0.948 0.948 -0.0664
#> 7 HvIpHG~9079 -0.809 0.294 0.598 -1.09
#> 8 JcKVfU~9653 0.642 0.365 0.598 0.932
#> 9 SGIVBl~5782 -0.494 0.484 0.622 -0.717