explore: Explore ATAC-seq data

In anthony-aylward/exploreatacseq: Exploratory Analysis of ATAC-seq data

Description

perform an exploratory analysis

Usage

explore(
  input_data,
  output_prefix,
  treatment_groups = list(),
  labels = FALSE,
  n_peaks = 1e+05,
  write_raw_counts = FALSE,
  write_transformed_counts = FALSE,
  write_counts = FALSE,
  cores = 1,
  palette_order = "categorical",
  palette = NULL
)

Arguments

input_data	list contatining data details or character path to a JSON file
output_prefix	character, a prefix for output files
treatment_groups	list providing groups of treatments to be compared
labels	if TRUE, text labels will be added to points in all plots
n_peaks	integer, number of the top most variable peaks to include in the analysis
write_raw_counts	logical, if TRUE the raw read count matrix will be written to disk as a TSV file
write_transformed_counts	logical, if TRUE the transformed read count matrix will be written to disk as a TSV file
write_counts	logical, if TRUE both raw and transformed read count matrices will be written to disk as TSV files
cores	integer, max number of cores to use
palette_order	ordering of color palette, eithier "categorical" or "sequential"
palette	the color palette

Details

The analysis consists of the following steps:

anthony-aylward/exploreatacseq documentation built on May 10, 2021, 8:45 a.m.