deseq_helper_functions.R

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#                                 HEADER
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# Author: Matthew Muller
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# Date: 2023-02-18
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# Script Name: DESeq2 Helper Functions
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# Notes:
# This script contains helper functions that can be used to assist in differential
# expression analysis using DESeq2. Most inputs are expected as DDS or SE objects.

message("This script is being deprecated. Please use the rna_functions and enrichment_functions scripts instead.")

message('
⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⣀⣀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⢀⣠⡤⠶⠭⠥⣼⣽⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⣠⠞⠉⠀⠀⠀⠀⠀⠀⠀⠉⠓⢦⡀⠀⠀⠀⠀⠀⠀
⠀⠀⡤⠞⢋⡟⣡⣤⠶⣶⡄⠀⠀⠀⢠⡶⠶⢦⣄⠙⣦⠤⢤⡀⠀⠀
⢀⡞⣡⢤⡾⠈⣵⠒⠶⢦⡀⢠⠖⠀⢠⡔⠒⠶⣮⠀⠘⣦⣤⡙⣆⠀
⢸⢿⡇⢰⠇⠀⠙⠒⠶⠋⢀⡏⠀⠀⠀⠙⠒⠚⠉⠀⠀⢹⠀⣹⠸⡆
⣾⠀⣉⢻⡄⠀⠀⠀⠀⣸⣼⣆⠀⣸⣤⡆⠀⠀⠀⠀⠀⢸⠞⠁⠀⢷
⠈⠉⠉⠛⢷⡀⠀⠀⠰⣿⣿⣿⣿⣿⣿⣿⠀⠀⠀⠀⠀⡼⠶⠚⠛⠋
⠀⠀⠀⠀⠀⠳⣄⠀⠀⠀⠀⠀⠉⠀⠈⠁⠀⠀⠀⣠⠞⠁⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠈⠛⠦⣄⣀⠀⠀⠀⠀⣀⣠⡴⠚⠁⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⣠⢾⣈⠉⠉⢉⣉⣁⡿⢤⡀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⡟⠀⠈⠉⠉⠉⠉⠁⠀⠈⣧⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⢀⣠⠤⠶⠚⠁⠀⠦⠤⠤⠤⠤⠖⠂⠀⠈⠓⠦⢤⣀⠀⠀⠀
⠀⢀⡞⠋⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠈⠳⣄⠀
⢀⡞⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠹⡆
⣸⠀⠀⠀⢀⡇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣇⠀⠀⠀⠀⣷
⡏⠀⠀⠀⢸⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢹⠀⠀⠀⠀⢸
⠃⠀⠀⠀⠛⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢘⠁⠀⠀⠀⠘
')

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#                                 CODE
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# the code has been moved to the filtering_functions, rna_functions, and enrichment_functions scripts
source('https://raw.githubusercontent.com/mattmuller0/Rtools/main/filtering_functions.R')
source('https://raw.githubusercontent.com/mattmuller0/Rtools/main/rna_functions.R')
source('https://raw.githubusercontent.com/mattmuller0/Rtools/main/enrichment_functions.R')