Proteomics Label Free Quantification

Documentation for package ‘prolfqua’ version 0.99.2

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-- A --

adjust_p_values	adjust columns
AggregateLimpa	AggregateLimpa
AggregateMedpolish	AggregateMedpolish
AggregateRlm	AggregateRlm
AggregateTopN	AggregateTopN
AnalysisConfiguration	Analysis Configuration
annotation_add_contrasts	DRY function: process and export annotated contrasts
AnovaExtractor	R6 class for extracting ANOVA results as a data frame

-- B --

build_contrast_analysis	Build a contrast analysis using one of several statistical methods
build_model	Build protein models from data
build_model_glm_peptide	Build Firth logistic model for nested LFQData
build_model_glm_protein	Build Firth logistic model for aggregated LFQData
build_model_impute	Build protein models with LOD imputation for failed fits
build_model_limma	Build limma model from LFQData
build_model_limma_impute	Build limma model with LOD imputation for failed proteins
build_model_limma_voom	Build limma model with vooma precision weights (proteomics)
build_model_limma_voom_impute	Build limma-voom model with LOD imputation for failed proteins
build_model_limpa	Build limpa vooma model from aggregated LFQData

-- C --

center_to_reference_cfg	center to reference
ContrastConfiguration	Contrast Configuration
Contrasts	Estimate contrasts using Wald Test
ContrastsBinomialNestedFacade	Quasibinomial detection-count facade for nested input
ContrastsDEqMSFacade	DEqMS contrast analysis facade
ContrastsDEqMSVoomFacade	DEqMS contrast analysis with vooma weights facade
ContrastsFirth	Estimate contrasts using Wald Test
ContrastsFirthFacade	Firth logistic missingness contrast analysis facade
ContrastsFirthNestedFacade	Firth logistic missingness contrast analysis facade for nested input
ContrastsInterface	Base class for all Contrasts classes
ContrastsLimma	Limma-based contrasts (direct limma pipeline)
ContrastsLimmaFacade	Limma contrast analysis facade
ContrastsLimmaImputeFacade	Limma contrast analysis with LOD imputation facade
ContrastsLimmaVoomFacade	Limma-voom contrast analysis facade
ContrastsLimmaVoomImputeFacade	Limma-voom contrast analysis with LOD imputation facade
ContrastsLimpaFacade	Limpa contrast analysis facade
ContrastsLimpaNestedFacade	Limpa contrast analysis facade for nested input
ContrastsLmerNestedFacade	Lmer (mixed-model) contrast analysis facade for nested input
ContrastsLMFacade	LM contrast analysis facade
ContrastsLMImputeFacade	LM contrast analysis with LOD imputation facade
ContrastsModerated	Limma moderated contrasts
ContrastsModeratedDEqMS	DEqMS count-dependent moderated contrasts
ContrastsPlotter	plot contrasts
ContrastsRfitFacade	Rfit rank-based regression contrast analysis facade
ContrastsRfitImputeFacade	Rfit rank-regression contrast analysis with LOD imputation facade
ContrastsRLMFacade	RLM contrast analysis facade
ContrastsROPECA	ROPECA reproducibility-optimization method
ContrastsROPECANestedFacade	ROPECA contrast analysis facade for nested input
ContrastsTable	holds results when contrasts are added.

-- D --

df.residual.rfit_prolfqua

Residual degrees of freedom for an augmented rfit fit

-- F --

FACADE_REGISTRY	Registry of available contrast facade classes
find_package_file	find file stored in package

-- G --

generate_contrasts	Combined generate_contrasts
generate_contrasts_for_factor	Single-factor contrasts (pairwise comparisons)
get_uniprot_id_from_fasta_header	Extracts uniprot ID
group_label	group label function

-- H --

HierarchyCountsSample

Count distinct elements for each level of hierarchy per sample

-- I --

impute_from_model	Fill missing responses with predictions from per-subject linear models
interaction_contrasts	Interaction contrasts (difference of differences)
INTERNAL_FUNCTIONS_BY_FAMILY	Internal Functions by category
is_contaminant	Detect contaminant identifiers
is_decoy	Detect decoy / reverse-database identifiers

-- L --

level_specific_contrasts	Level-specific contrasts (per secondary level)
LFQData	LFQData R6 class
LFQDataPlotter	LFQDataPlotter - Create various visualization of the LFQdata
LFQDataStats	Decorates LFQData with methods to compute statistics of interactions
LFQDataSummariser	Summarize LFQData
LFQDataToSummarizedExperiment	converts LFQData object to SummarizedExperiment
LFQDataTransformer	Decorate LFQData with Methods for transforming Intensities
list_facades	List currently registered contrast facades
list_to_AnalysisConfiguration	read minimal yaml to reconstruct configuration
list_to_ContrastConfiguration	Rebuild a ContrastConfiguration from a list
lookup_facade	Look up a contrast facade by short name
LR_test	Likelihood ratio test

-- M --

main_effect_contrasts	main effects contrasts
matrix_to_tibble	matrix or data.frame to tibble (taken from tidyquant)
merge_contrasts_results	Merge contrast results coming from two different model.
MissingHelpers	Group statistics and limit of detection
Model	R6 class representing modelling result
ModelFirth	R6 class representing modelling result
ModelInterface	R6 interface class representing modelling result
ModelLimma	R6 class representing a limma modelling result

-- N --

nr_children_experiment	Max nr_children across samples per hierarchy unit
nr_features_experiment	Count distinct child features per hierarchy unit
nr_obs_sample	Aggregates e.g. protein abundances from peptide abundances

-- P --

PACKAGE_DATA	Package Data
pivot_model_contrasts_to_wide	pivot model contrasts matrix to wide format produced by 'contrasts_linfct' and ...
prolfqua_data	load data from prolfqua

-- R --

R6_extract_values	Extract all value slots in an R6 object
register_facade	Register a contrast facade class

-- S --

setup_analysis	Setup a tidy table compatible with a 'AnalysisConfiguration'
sigma.rfit_prolfqua	Scale estimate for an augmented rfit fit
sim_lfq_data	simulate protein level data with two groups
sim_lfq_data_2factor_config	Simulate data, protein, with config with 2 factors Treatment and Background
sim_lfq_data_peptide_config	Simulate data, protein and peptide, with config
sim_lfq_data_protein_config	Simulate data, protein, with config
StrategyBinomial	Quasibinomial detection-count strategy
StrategyLimma	R6 class for limma modelling strategy
StrategyLimpa	R6 class for limpa modelling strategy
StrategyLM	Linear model strategy (R6 class)
StrategyLmer	Linear mixed-effects model strategy (R6 class)
StrategyLogistf	Firth's logistic regression strategy (R6 class)
StrategyRfit	Rank-based regression strategy (R6 class)
StrategyRLM	Robust linear model strategy (R6 class)
strategy_binomial	Create a quasibinomial detection-count strategy
strategy_limma	Create limma modelling strategy
strategy_limpa	Create limpa modelling strategy
strategy_lm	Create Firth's logistic regression strategy
strategy_lmer	Create Firth's logistic regression strategy
strategy_logistf	Create Firth's logistic regression strategy
strategy_rfit	Create Firth's logistic regression strategy
strategy_rlm	Create Firth's logistic regression strategy
summarize_stats_factors	compute var sd etc for all factor levels

-- T --

table_facade

table facade to easily switch implementations

-- U --

upset_interaction_missing_stats

UpSetR plot from interaction_missing_stats

-- V --

vcov.rfit_prolfqua	Named variance-covariance matrix for an augmented rfit fit
volcano_plotly	volcano plotly

-- W --

which_missing

add missing values to x vector based on the values of x