calc_cutoffs_from_profiles: Calculate offsets from 5'end profiles

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

Calculate offsets from 5'end profiles

Description

This function calculates cutoffs and frame resolution for Ribo-seq reads, for each read length and compartment.

Usage

calc_cutoffs_from_profiles(reads_profile, length_max)

Arguments

reads_profile	Profile of 5'ends around start and stop codon, as a DataFrame object with tx_ids as rows and positions as columns
length_max	Maximum cutoff to use

Details

Three methods are used and combined in the final choice: the position of maximum coverage around start codon is calculated for each transcript, and the most frequent one is stored in the "*_tab" objects. Such frequency values are also subjected to k-means clustering (centers=3) and the first value belonging to the highest cluster is selected, output as "*km_tab" objects. Analysis of aggregate plots, instead of frequencies, is performed again using kmeans (centers=3) using the same analysis above and stored in the "*km_meta" objects, and by simply calculating the maximum value in the profile, stored in the "*meta" objects. for each method, all reads ("absolute_") or only in-frame positions ("in_frame_") are considered. The final choice takes the most frequent cutoff chosen in all methods applied to in-frame positions.

Value

a list with a final_cutoff object, the frame analysis containing the displaying the max frame and the average all the calculated cutoffs in cutoffs, data used for the frame analysis in frames, and profiles around start codons in profiles_start.

Author(s)

Lorenzo Calviello, [e-mail]

See Also

RiboseQC_analysis

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