Differential Abundance Analysis of Label-Free Mass Spectrometry Data

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Documentation for package ‘proDA’ version 1.19.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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$-method	Fluent use of accessor methods
$<--method	Fluent use of accessor methods
.DollarNames.proDAFit	Fluent use of accessor methods
.proDAFit	proDA Class Definition
abundances	Get the abundance matrix
abundances-method	Get different features and elements of the 'proDAFit' object
accessor_methods	Get different features and elements of the 'proDAFit' object
coefficients	Get the coefficients
coefficients-method	Get different features and elements of the 'proDAFit' object
coefficient_variance_matrices	Get the coefficients
coefficient_variance_matrices-method	Get different features and elements of the 'proDAFit' object
convergence	Get the convergence information
convergence-method	Get different features and elements of the 'proDAFit' object
design-method	Get different features and elements of the 'proDAFit' object
dist_approx	Calculate an approximate distance for 'object'
dist_approx-method	Distance method for 'proDAFit' object
dist_approx_impl	Distance method for 'proDAFit' object
dollar_methods	Fluent use of accessor methods
feature_parameters	Get the feature parameters
feature_parameters-method	Get different features and elements of the 'proDAFit' object
generate_synthetic_data	Generate a dataset according to the probabilistic dropout model
hyper_parameters	Get the hyper parameters
hyper_parameters-method	Get different features and elements of the 'proDAFit' object
invprobit	Inverse probit function
median_normalization	Column wise median normalization of the data matrix
pd_lm	Fit a single linear probabilistic dropout model
pd_row_f_test	Row-wise tests of difference using the probabilistic dropout model
pd_row_t_test	Row-wise tests of difference using the probabilistic dropout model
predict-method	Predict the parameters or values of additional proteins
proDA	Main function to fit the probabilistic dropout model
proDAFit-class	proDA Class Definition
proDA_package	proDA: Identify differentially abundant proteins in label-free mass spectrometry
reference_level	Get the reference level
reference_level-method	Get different features and elements of the 'proDAFit' object
result_names	Get the result_names
result_names-method	Identify differentially abundant proteins
test_diff	Identify differentially abundant proteins