wolski/prolfqua
Proteomics Label Free Quantification

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wolski/prolfqua: Proteomics Label Free Quantification
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API

API for wolski/prolfqua
Proteomics Label Free Quantification

Global functions
.ExtractMatrix Source code
.checkForFile Source code
.coeff_weights_factor_levels Source code
.dircleaner Source code
.dirmaker Source code
.ehandler Source code Source code
.extractInt Source code
.generate_random_string Source code
.get_match_idx Source code
.get_robscales Man page Source code
.get_sides Source code
.lfq_power_t_test_quantiles Source code
.likelihood_ratio_test Source code
.lmer4_coeff_matrix Source code
.make_name_AinB Source code
.missigness_impute_interactions Man page Source code
.multigroup_volcano Source code
.nr_B_in_A Source code
.partial_AUC_summary Source code
.plot_ROC Source code
.plot_precision_recall Source code
.plot_score_distribution Source code
.rankProteinPrecursors Source code
.reestablish_condition Source code
.rlm_estimate Source code
.run_markdown_with_params Source code
.scale_probabilities Source code
.squeezeVarRob Source code
.summarise_missing_contrasts Man page Source code
AnalysisConfiguration Man page
AnalysisParameters Man page
AnalysisTableAnnotation Man page
Benchmark Man page
Contrasts Man page
ContrastsInterface Man page
ContrastsMissing Man page
ContrastsModerated Man page
ContrastsPlotter Man page
ContrastsProDA Man page
ContrastsROPECA Man page
ContrastsTable Man page
INTERNAL_FUNCTIONS_BY_FAMILY Man page
LFQData Man page
LFQDataAggregator Man page
LFQDataPlotter Man page
LFQDataStats Man page
LFQDataSummariser Man page
LFQDataToSummarizedExperiment Man page Source code
LFQDataTransformer Man page
LFQDataWriter Man page
LR_test Man page Source code
MissingHelpers Man page
Model Man page
ModelInterface Man page
PACKAGE_DATA Man page
ProjectStructure Man page
ProteinAnnotation Man page
R6_extract_values Man page Source code
UpSet_interaction_missing_stats Man page Source code
UpSet_missing_stats Man page Source code
adjust_p_values Man page Source code
aggregate_contrast Man page Source code
aggregate_intensity_topN Man page Source code
apply_to_response_matrix Man page Source code
build_model Man page Source code
complete_cases Man page Source code
compute_pooled Man page Source code
concrete_AnalysisConfiguration Man page
contrasts_fisher_exact Man page Source code
contrasts_linfct Man page Source code
cor_jackknife_matrix Man page Source code
cor_order Man page Source code
create_config_MQ_peptide Man page Source code
create_config_MSFragger_MSstats Man page Source code
create_config_Skyline Man page Source code
create_config_Spectronaut_Peptide Man page Source code
data_IonstarProtein_subsetNorm Man page
data_SAINTe_output Man page
data_Yeast2Factor Man page
data_basicModel_p1807 Man page
data_benchmarkExample Man page
data_checksummarizationrobust87 Man page
data_checksummarizerobust Man page
data_checksummarizerobust69 Man page
data_correlatedPeptideList Man page
data_factor_levelContrasts Man page
data_interactionModel_p1807 Man page
data_ionstar Man page
data_modellingResult_A Man page
data_multigroupFC Man page
data_skylinePRMSample_A Man page
data_skylineSRM_HL_A Man page
data_spectronautDIA250_A Man page
data_test_confusion_matrix_scores Man page
do_confusion Source code
do_confusion_c Source code
estimate_intensity Man page Source code
filter_byQValue Man page Source code
filter_difference Man page Source code
filter_proteins_by_peptide_count Man page Source code
find_package_file Man page Source code
fitFDistRobustly_LG Source code
fitFDist_LG Source code
get_UniprotID_from_fasta_header Man page Source code
get_anova_df Man page Source code
get_complete_model_fit Man page Source code
get_contrast Man page Source code
get_impute_contrasts_V1 Source code
get_imputed_contrasts Man page Source code
get_p_values_pbeta Man page Source code
get_robscales Man page Source code
hierarchy_counts Man page Source code
hierarchy_counts_sample Man page Source code
intensity_summary_by_hkeys Man page Source code
interaction_missing_stats Man page Source code
ionstar_bench_preprocess Man page Source code
isSingular_lm Man page Source code
jackknife Man page Source code
jackknife_matrix Man page Source code
lfq_power_t_test_proteins Man page Source code
lfq_power_t_test_quantiles Man page Source code
lfq_power_t_test_quantiles_V2 Man page Source code
lfq_write_table Man page Source code
linfct_all_possible_contrasts Man page Source code
linfct_factors_contrasts Man page Source code
linfct_from_model Man page Source code
linfct_matrix_contrasts Man page Source code
make_benchmark Man page Source code
make_interaction_column Man page Source code
make_reduced_hierarchy_config Man page Source code
matrix_to_tibble Man page Source code
medpolish_estimate Man page Source code
medpolish_estimate_df Man page Source code
medpolish_estimate_dfconfig Man page Source code
medpolish_protein_estimates Man page Source code
merge_contrasts_results Man page Source code
missigness_histogram Man page Source code
missigness_impute_factors_interactions Man page Source code
missingness_per_condition Man page Source code
missingness_per_condition_cumsum Man page Source code
model_analyse Man page Source code
model_summary Man page Source code
moderated_p_limma Man page Source code
moderated_p_limma_long Man page Source code
ms_bench_add_scores Man page Source code
ms_bench_auc Man page Source code
multigroup_volcano Man page Source code
my_contest Man page Source code
my_contrast Man page Source code
my_contrast_V1 Man page Source code
my_contrast_V2 Man page Source code
my_glht Man page Source code
names_to_matrix Man page Source code
normalize_log2_robscale Man page Source code
nr_B_in_A Man page Source code
nr_B_in_A_per_sample Man page Source code
nr_obs_experiment Man page Source code
nr_obs_sample Man page Source code
old2new Man page Source code
pairs_smooth Man page
pairs_w_abline Man page Source code
panel_cor Man page Source code
panel_hist Man page Source code
pivot_model_contrasts_2_Wide Man page Source code
plot_NA_heatmap Man page Source code
plot_estimate Man page Source code
plot_heatmap Man page Source code
plot_heatmap_cor Man page Source code
plot_hierarchies_add_quantline Man page Source code
plot_hierarchies_boxplot Man page Source code
plot_hierarchies_boxplot_df Man page Source code
plot_hierarchies_line Man page Source code
plot_hierarchies_line_default Source code
plot_hierarchies_line_df Man page Source code
plot_intensity_distribution_density Man page Source code
plot_intensity_distribution_violin Man page Source code
plot_lmer_model_and_data Man page Source code
plot_lmer_peptide_noRandom Man page Source code
plot_lmer_peptide_predictions Man page Source code
plot_lmer_predicted_interactions Man page Source code
plot_pca Man page Source code
plot_raster Man page Source code
plot_sample_correlation Man page Source code
plot_screeplot Man page Source code
plot_stat_density Man page Source code
plot_stat_density_median Man page Source code
plot_stat_violin Man page Source code
plot_stat_violin_median Man page Source code
plot_stdv_vs_mean Man page Source code
pooled_V1 Man page Source code
pooled_V2 Man page Source code
poolvar Man page Source code
prolfqua_data Man page
rank_by_NA Man page Source code
rank_peptide_by_intensity Man page Source code
remove_NA_rows Man page Source code
remove_large_QValues Man page Source code
remove_small_intensities Man page Source code
render_MQSummary_rmd Man page Source code
response_as_matrix Man page Source code
response_matrix_as_tibble Man page Source code
rlm_estimate Man page Source code
rlm_estimate_dfconfig Man page Source code
robust_scale Man page Source code
sample_subset Man page Source code
scale_with_subset Man page Source code
scale_with_subset_by_factors Man page Source code
scriptCopyHelperVec Man page Source code
separate_factors Man page Source code
separate_hierarchy Man page Source code
setup_analysis Man page Source code
sim_lfq_data Man page Source code
sim_lfq_data_peptide_config Man page Source code
sim_lfq_data_protein_2Factor_config Man page Source code
sim_lfq_data_protein_config Man page Source code
spread_response_by_IsotopeLabel Man page Source code
squeezeVarRob Man page Source code
strategy_glm Man page Source code
strategy_lm Man page Source code
strategy_lmer Man page Source code
strategy_rlm Man page Source code
summarise_QValues Man page Source code
summarize_hierarchy Man page Source code
summarize_stats Man page Source code
summarize_stats_all Man page Source code
summarize_stats_factors Man page Source code
summarize_stats_quantiles Man page Source code
summary_ROPECA_median_p.scaled Man page Source code
table_facade Man page
table_factors Man page Source code
tidy_to_wide Man page Source code
tidy_to_wide_config Man page Source code
transform_work_intensity Man page Source code
volcano_plotly Man page
which_missing Man page Source code
wolski/prolfqua documentation built on April 27, 2024, 4:09 p.m.

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