scNucleosomeQC: Quality Control for Nucleosome Signal per Cell

In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

Quality Control for Nucleosome Signal per Cell

Description

Quality Control for Nucleosome Signal per Cell

Usage

scNucleosomeQC(frags = NULL, n = NULL, verbose = TRUE, ...)

Arguments

frags	A Fragment object. If the Fragment object contains "cells" slot, the output will be filtered by "cells" slot. if not, all cells are reported.
n	Number of lines to read from the fragment file. If NULL, read all lines. Default: (cellnumber * 5e3) or 4e7.
verbose	Display messages, TRUE or FALSE
...	Arguments passed to other functions

Details

Calculate the strength of the nucleosome signal per cell. Computes the ratio of fragments between 147 bp and 294 bp (mononucleosome) to fragments < 147 bp (nucleosome-free)

Value

Returns a dataframe for mononucleosomal, nucleosome_free, nucleosome_signal and nucleosome_percentile of each cell.

wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.