IndelIdents: IndelIdents

In mana-W/LinTInd: Lineage tracing by indels

Description

Function to define a scarform for each cell(single cell) or each reads(bulk seq, generate 'cell barcode' for each reads)

Usage

IndelIdents(scarinfo, method.use = NULL, cln)

Arguments

scarinfo	List generate from IndelForm, for more see IndelForm
method.use	Select how to determine a scar form string for each cell: "reads.num" (default):find the scar with the most reads in the cell; "umi.num":find the scar with the most UMIs in the cell; "consensus":find the consistent sequences in each cell, and then generate scar form strings from the new reads
cln	The number of threads

Details

Title

Value

The list generate from FindIndel, but in 'Scar' element a new column contain scar form strings

Examples

data("example_data",package = "LinTInd")
IndelIdents(scarinfo,method.use="umi.num",cln=1)

mana-W/LinTInd documentation built on Feb. 14, 2022, 10:13 a.m.