SCQC: Get Single Cell Pre-processing Information

SCQCR Documentation

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.