AggregateTiles: Quantify aggregated genome tiles

Description Usage Arguments Value

View source: R/generics.R

Description

Quantifies fragment counts per cell in fixed-size genome bins across the whole genome, then removes bins with less than a desired minimum number of counts in the bin, then merges adjacent tiles into a single region.

Usage

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AggregateTiles(object, ...)

## S3 method for class 'Seurat'
AggregateTiles(
  object,
  genome,
  assay = NULL,
  new.assay.name = "tiles",
  min_counts = 5,
  binsize = 5000,
  verbose = TRUE,
  ...
)

## S3 method for class 'ChromatinAssay'
AggregateTiles(
  object,
  genome,
  min_counts = 5,
  binsize = 5000,
  verbose = TRUE,
  ...
)

## Default S3 method:
AggregateTiles(
  object,
  genome,
  cells = NULL,
  min_counts = 5,
  binsize = 5000,
  verbose = TRUE,
  ...
)

Arguments

object

A Seurat object or ChromatinAssay object

...

Additional arguments passed to other methods

genome

genome A vector of chromosome sizes for the genome. This is used to construct the genome bin coordinates. The can be obtained by calling seqlengths on a BSgenome-class object.

assay

Name of assay to use

new.assay.name

Name of new assay to create containing aggregated genome tiles

min_counts

Minimum number of counts for a tile to be retained prior to aggregation

binsize

Size of the genome bins (tiles) in base pairs

verbose

Display messages

cells

Cells to include

Value

When running on a Seurat object, returns the Seurat object with a new ChromatinAssay added.

When running on a ChromatinAssay, returns a new ChromatinAssay containing the aggregated genome tiles.

When running on a fragment file, returns a sparse region x cell matrix.


timoast/signac documentation built on Dec. 14, 2021, 11:34 p.m.