range_counts {segmenter}R Documentation

Format the loaded counts data

Description

The function takes the data.frames of the loaded counts data and format them into GRanges or SummarizedExperiment objects.

Usage

range_counts(
  counts,
  features,
  return = "GRanges",
  tidy = FALSE,
  average = FALSE,
  marks
)

Arguments

counts

A matrix of the read_bam_file output.

features

A GRanges. That was used to count the bam files.

return

A string. Possible values are GRanges (default) or SummarizedExperiment.

tidy

A logical. Default is TRUE. Whether to tidy the metadata columns of the GRanges object.

average

A logical. Default is FALSE. Whether to average the counts by marks before building the object.

marks

A character vector. The length shoud equal the numbe of columns in counts and is used for averaging and renaming the matrix columns.

Value

GRanges (default) or SummarizedExperiment.


[Package segmenter version 1.0.0 Index]