AggregateTiles: Quantify aggregated genome tiles

In timoast/signac: Analysis of Single-Cell Chromatin Data

Quantify aggregated genome tiles

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

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 Aug. 23, 2024, 1:48 a.m.