SCQC: Get Single Cell Pre-processing Information

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

Get Single Cell Pre-processing Information

Description

Get scATAC-seq pre-processing results and create Fragment Object.

Usage

atacSCQC(
  atacProcFrag,
  atacProcPeak,
  fragInput = NULL,
  csvInput = NULL,
  peak = NULL,
  gene.annotation = NULL,
  blacklist = NULL,
  n = 2000,
  ...
)

## S4 method for signature 'ATACProc'
atacSCQC(
  atacProcFrag,
  atacProcPeak,
  fragInput = NULL,
  csvInput = NULL,
  peak = NULL,
  gene.annotation = NULL,
  blacklist = NULL,
  n = 2000,
  ...
)

atacscQC(
  fragInput = NULL,
  csvInput = NULL,
  peak = NULL,
  gene.annotation = NULL,
  blacklist = NULL,
  n = 2000,
  ...
)

Arguments

atacProcFrag	ATACProc-class object scalar. It has to be the return value of upstream process: ###################
atacProcPeak	ATACProc-class object scalar. It has to be the return value of upstream process: ###################
fragInput	scATAC-seq fragment file.
csvInput	scATAC-seq csv record file.
peak	scATAC-seq peak file in BED format.
gene.annotation	scATAC-seq gene.annotation file in BED format. Note: Please using the results from function GetGRangesFromEnsDb or using the default data.
blacklist	Genome blacklist file in BED format.
n	Number of regions to process at a time. Default: 2000.
...	Additional arguments, currently unused.

Value

An invisible ATACProc-class object scalar.

Author(s)

Wei Zhang

Examples

print(123)

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