choose_readlengths: Filter read lengths for P-sites position calculation

In ohlerlab/RiboseQC: RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

Filter read lengths for P-sites position calculation

Description

This function selects a subset of readlenghts to be used in the P-sites calculation step

Usage

choose_readlengths(summary_data, choice = "max_coverage", nt_signals)

Arguments

summary_data	output data from the calc_cutoffs_from_profiles function
choice	Method used to select readlengths, defaults to "max_coverage"
nt_signals	Profiles of 5'ends around start codons

Details

Three different methods are available to choose readlengths: the "max_coverage" method selects all read lenghts with more in-frame signal compared to out-of-frame signal, on all codons; the "max_inframe" method starts with the most accurate read length and progressively selects read lengths which add in-frame signals in codons not covered by previous read lengths; the "all" method selects all available read lengths

Value

a list object containing different compartments. Each sub-list contains final_choice, the set of chosen read lengths with cutoffs, and data, the complete stats for each selection method

Author(s)

Lorenzo Calviello, [e-mail]

See Also

calc_cutoffs_from_profiles

ohlerlab/RiboseQC documentation built on Aug. 15, 2023, 7:30 a.m.