index_peaks_barcodes_to_matrix_indexes: Read index-peaks-barcodes trio files on interval to create...

In ChromSCape: Analysis of single-cell epigenomics datasets with a Shiny App

Description

Read index-peaks-barcodes trio files on interval to create count indexes

Usage

index_peaks_barcodes_to_matrix_indexes(
  peak_file,
  index_file,
  name_cells,
  binarize = FALSE,
  ref = "hg38"
)

Arguments

peak_file	A file containing the peak genomic locations
index_file	A file containing the indexes of non-zeroes values and their value (respectively i,j,x,see sparseMatrix)
name_cells	A vector with cell names
binarize	Binarize matrix ?
ref	Reference genome

Value

A list containing a "feature index" data.frame and a region GenomicRange object both used to form the sparse matrix

ChromSCape documentation built on Nov. 8, 2020, 6:57 p.m.