countRemoveOrganelle: countRemoveOrganelle

In plantformatics/Socrates: Analysis of scATAC-seq data

countRemoveOrganelle

Description

This functions takes in an the Tn5 bed file, as well as obj vector which contains organelle scaffolds, and identifies Tn5 integrations events which occured in organelles. These reads are then assigned to the object slot PtMT. Additional parameters allow for the removal of these reads so they don't interfere with ACR calling downstream.

Usage

countRemoveOrganelle(obj, org_scaffolds = NULL, remove_reads = FALSE)

Arguments

obj	Object output from loadBEDandGenomeData. Required.
org_scaffolds	vector of organelle scaffold names
remove_reads	Logical of whether to remove reads from the BED file or not. Defaults to TRUE

plantformatics/Socrates documentation built on April 3, 2025, 1:02 p.m.