CalculateBandingScore: Calculate Banding scores for all cells

In crazyhottommy/scATACutils: What the Package Does (One Line, Title Case)

Description

A banding score is a measure signals of nucleosomal periodicity in their fragment size distribution. see Darren et.al.2018 The input of this function is calculated by a python script: get_insert_size_distribution_per_cell.py possorted_bam.bam pbmc_5k_insert_size.txt –barcodes barcodes.tsv

Usage

CalculateBandingScore(df, barcodeList = NULL)

Arguments

df	A dataframe with 3 columns. cell column contains the cell barcode for all cells, insert_size column contains the insert size, read_count column contains the number of paired reads for that insert size
barcodeList	a vector of valid barcodes. e.g. the first column of barcodes.tsv from 10x

Value

Banding scores for all cells.

crazyhottommy/scATACutils documentation built on June 15, 2020, 9:31 p.m.