Differential Abundance Analysis of Label-Free Mass Spectrometry Data

[Up] [Top]

Documentation for package ‘proDA’ version 1.7.0

Help Pages

$-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