SingleFileCutMatrix: Generate matrix of integration sites
In wzthu/ATACpipe: An Easy-to-use Systematic pipeline for ATACseq data analysis

SingleFileCutMatrix

R 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.