SingleFileCutMatrix: Generate matrix of integration sites

SingleFileCutMatrixR Documentation

Generate matrix of integration sites

Description

Generate matrix of integration sites

Usage

SingleFileCutMatrix(cellmap, region, cells = NULL, tabix.file, verbose = TRUE)

Arguments

cellmap

A mapping of cell names in the fragment file to cell names in the Seurat object. Should be a named vector where each element is a cell name that appears in the fragment file and the name of each element is the name of the cell in the Seurat object.

region

A set of GRanges containing the regions of interest

cells

Which cells to include in the matrix. If NULL, use all cells in the cellmap

tabix.file

A TabixFile object.

verbose

Display messages

Details

Generates a cell-by-position matrix of Tn5 integration sites centered on a given region (usually a DNA sequence motif). This matrix can be used for downstream footprinting analysis.

Value

Returns a sparse matrix


wzthu/ATACpipe documentation built on Aug. 12, 2022, 7:38 a.m.