differential_expression: Differential gene expression analysis

In irilenia/baerhunter: Detection and Analysis of Expressed Intergenic Elements in Bacterial RNA-seq Data

Differential gene expression analysis

Description

A wrapper function to perform analysis of differential gene expression using DESeq2 method.

Usage

differential_expression(
  feature_count_file,
  metadata_file,
  cutoff_value,
  multiple_variables,
  main_condition,
  output_file_name
)

Arguments

feature_count_file	A CSV file containing a table of counts for a particular feature type.
metadata_file	A file outlining the experimental conditions for each sample.
cutoff_value	Retain only the genes that have at least half the samples with the counts above the cut-off value.
multiple_variables	A boolean indicating if the experimental design contained more than one condition.
main_condition	A string indicating which of the conditions is the most important; should coincide with the name in the metadata table.
output_file_name	A string containing the name of the output file.

Value

DESeq result table and the result summary are written into separate files. Summary file name is derived from the provided output file name with an addition of "summary.txt".

irilenia/baerhunter documentation built on May 18, 2024, 11:56 p.m.