beat: Beat

In thekuhninator/beat: A Package for Assessing the Magnitute of the Batch Effect in RNA-Seq Data.

Description

Takes in gene counts, metadata, and output paths, as well as a dataset name and outputs an html report.

Usage

beat(input_counts, input_metadata, output_dir, dataset_name, original)

Arguments

input_counts	the path to the gene counts with rows as genes and columns as samples
input_metadata	the path to the metadata with attributes as columns and the samples as the rows, with the first row having the id of each sample.
output_dir	the path to the folder where the output files and output report will be generated.
dataset_name	the name of the dataset to be used in the report and plots.
original	boolean representing if these are the uncorrected counts. (If using multibeat there should only be one original)

thekuhninator/beat documentation built on Oct. 11, 2021, 10:54 a.m.