All functions

PPplot

Creates PP plot of two empirical distributions.

calculate_fdr

Calculates qvalues on the subset PSMs.

dpi0

Density function for the \(\pi_0\) distribution.

id_is_present

Checks if protein id appears in the headers of a fasta file.

parse_msgf_mzid

Parses a mzID file generated by MS-GF+.

pi0plot

Creates density plot of the pi0 distribution.

plot_diag

Plot diagnostic plots to evaluate assumptions from the search all, search subset strategy.

preprocess

Preprocess data from a MS-GF mzID file.

rpi0

Random generation for the \(\pi_0\) distribution.

saas_gui

Launches the GUI version of saas.

simulate_subset

Random generation of a dataset after TDA.