make_atac_cds: Make ATAC CDS object

In cicero: Precict cis-co-accessibility from single-cell chromatin accessibility data

Description

This function takes as input a data frame or a path to a file in a sparse matrix format and returns a properly formatted CellDataSet (CDS) object.

Usage

make_atac_cds(input, binarize = FALSE)

Arguments

input

Either a data frame or a path to input data. If a file, it should be a tab-delimited text file with three columns and no header. For either a file or a data frame, the first column is the peak coordinates in the form "chr10_100013372_100013596", the second column is the cell name, and the third column is an integer that represents the number of reads from that cell overlapping that peak. Zero values do not need to be included (sparse matrix format).

binarize

Logical. Should the count matrix be converted to binary?

Value

A CDS object containing your ATAC data in proper format.

Examples

  data("cicero_data")
  input_cds <- make_atac_cds(cicero_data, binarize = TRUE)

cicero documentation built on Dec. 10, 2020, 2 a.m.