millipede_binning: Performs 'MILLIPEDE' binning on count matrix

In HarteminkLab/TOP: Predict transcription factor occupancy using DNase- or ATAC-seq data

Performs MILLIPEDE binning on count matrix

Description

Performs binning using different MILLIPEDE binning schemes (M5, M24, M12, M3, M2, M1) on the input count matrix.

Usage

millipede_binning(
  counts,
  bin_method = c("M5", "M24", "M12", "M3", "M2", "M1"),
  combine_strands = c("vertical", "motif")
)

Arguments

counts	DNase-seq or ATAC-seq read counts matrix, rows are candidate sites, columns are DNase or ATAC counts with 100bp flanks around motifs on the forward and reverse strands.
bin_method	MILLIPEDE binning scheme. Options: ‘M5’ (default), ‘M24’, ‘M12’, ‘M3’, ‘M2’, and ‘M1’.
combine_strands	Method to combine counts on both strands from M24 bins to M12 bins: ‘vertical’ (combine counts from both strands vertically) or ‘motif’ (combine counts from both strands with respect to motif match orientation).

Value

A list containing binning results (data frames) using different binning schemes.

Examples

## Not run: 
# Performs MILLIPEDE binning with different binning schemes.

# M5 binning
M5_bins <- millipede_binning(counts, bin_method = 'M5')

## End(Not run)

HarteminkLab/TOP documentation built on July 27, 2023, 6:14 p.m.