addAtacObj: Creat additional slots for atac-seq analysis extended from an...
In huqiwen0313/snarePip: snarePip

addAtacObj

R Documentation

Creat additional slots for atac-seq analysis extended from an existing object

Description

Creat additional slots for atac-seq analysis extended from an existing object

Usage

addAtacObj(
  obj,
  pmat = NULL,
  fragments = NULL,
  promoterRegion = NULL,
  TSS = NULL,
  blacklist = NULL,
  exons = NULL,
  transcripts = NULL,
  enhancers = NULL,
  tool = "pagoda2"
)

Arguments

`obj`	existing object (paagoda2)
`pmat`	peak matrix - rows are cells colums are peaks (chr:start-end)
`promoterRegion`	GRanges object containing the promoter regions
`TSS`	GRanges object containing tss locations
`frament`	fragment file that has the same format as https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/output/fragments