read_aggregated_vplot-GRangesList-character-BSgenome-method: Read aggregated V-plot from a list of genomic ranges...
In gongx030/seatac: ATAC-seq V-plot analysis

read_aggregated_vplot,GRangesList,character,BSgenome-method

R Documentation

Read aggregated V-plot from a list of genomic ranges (GRangeList)

Description

This function is to quickly read aggregated V-plot given a list of GRanges (e.g. motif binding sites) for scATAC-seq.

Usage

## S4 method for signature 'GRangesList,character,BSgenome'
read_aggregated_vplot(
  x,
  filenames,
  genome,
  bin_size = 5L,
  fragment_size_range = c(80, 320),
  fragment_size_interval = 5L
)

Arguments

`x`	a GRangeList object that define a list of genomic region sets.
`filenames`	BAM file names
`genome`	a BSgenome object
`bin_size`	The bin size in base pairs (default: 5L)
`fragment_size_range`	The range of the PE reads fragment sizes (default: c(80L, 320L))
`fragment_size_interval`	Fragment size interval (default: 5L)