Aidan Coyle, afcoyle@uw.edu
Originally written 2021/01/29
Roberts Lab, UW-SAFS
Written for analysis of Hematodinium differential gene expression
This script produces the CSV needed for GO-MWU, which is a 2-column table of accession IDs and unadjusted p-values. A header line is required, although the contents are irrelevant.
GO-MWU also requires another input file which we already created - a tab-delimited 2-column table of accession IDs and GO terms with no header and only 1 line per gene
This script utilizes a function built for this analysis by me - geneids_pvals(). It is defined in hematodinium_analysis_functions.R
input_file: DESeq2 output file containing transcript IDs and unadjusted p-values
blast_file: path that leads to transcript ID/accession ID table. Optimally, use an annotated BLASTx table of the same transcriptome used to create the kallisto index
output_file: path to the output file - a 2-column CSV of accession IDs and unadjusted p-values with a header line. This should be written to the same directory that you will run GO-MWU in.
library(tidyverse)
source("hematodinium_analysis_functions.R")geneIDs_pvals(input_file = "../graphs/DESeq2_output/cbaihemat_transcriptomev2.0/elev2_vs_amb02_indiv_only/AllGenes_wcols.txt",
blast_file = "../data/cbai_hemat_diamond_blastx_table_transcriptome_v2.0.txt",
output_file = "../scripts/16_running_GO-MWU/cbaihemat2.0_elev2_vs_amb02_indiv_only_pvals.csv")
# Elevated Day 2 vs. Ambient Day 0+2+17 + Elevated Day 0 + Lowered Day 0
geneIDs_pvals(input_file = "../graphs/DESeq2_output/cbaihemat_transcriptomev2.0/amb0217_elev0_low0_vs_elev2/AllGenes_wcols.txt",
blast_file = "../data/cbai_hemat_diamond_blastx_table_transcriptome_v2.0.txt",
output_file = "../scripts/16_running_GO-MWU/cbaihemat2.0_amb0217_elev0_low0_vs_elev2_pvals.csv")
# Elevated Day 0 vs. Elevated Day 2, indiv. libraries only
geneIDs_pvals(input_file = "../graphs/DESeq2_output/cbaihemat_transcriptomev2.0/elev0_vs_elev2_indiv/AllGenes_wcols.txt",
blast_file = "../data/cbai_hemat_diamond_blastx_table_transcriptome_v2.0.txt",
output_file = "../scripts/16_running_GO-MWU/cbaihemat2.0_elev0_vs_elev2_indiv_pvals.csv")
# Ambient Day 0 vs. Ambient Day 2, indiv. libraries only
geneIDs_pvals(input_file = "../graphs/DESeq2_output/cbaihemat_transcriptomev2.0/amb0_vs_amb2_indiv/AllGenes_wcols.txt",
blast_file = "../data/cbai_hemat_diamond_blastx_table_transcriptome_v2.0.txt",
output_file = "../scripts/16_running_GO-MWU/cbaihemat2.0_amb0_vs_amb2_indiv_pvals.csv")
# Ambient Day 0 vs. Ambient Day 17, indiv. libraries only
geneIDs_pvals(input_file = "../graphs/DESeq2_output/cbaihemat_transcriptomev2.0/amb0_vs_amb17_indiv/AllGenes_wcols.txt",
blast_file = "../data/cbai_hemat_diamond_blastx_table_transcriptome_v2.0.txt",
output_file = "../scripts/16_running_GO-MWU/cbaihemat2.0_amb0_vs_amb17_indiv_pvals.csv")
# Ambient Day 2 vs. Ambient Day 17, indiv. libraries only
geneIDs_pvals(input_file = "../graphs/DESeq2_output/cbaihemat_transcriptomev2.0/amb2_vs_amb17_indiv/AllGenes_wcols.txt",
blast_file = "../data/cbai_hemat_diamond_blastx_table_transcriptome_v2.0.txt",
output_file = "../scripts/16_running_GO-MWU/cbaihemat2.0_amb2_vs_amb17_indiv_pvals.csv")
# Ambient Day 2 vs. Elevated Day 2, indiv. libraries only
geneIDs_pvals(input_file = "../graphs/DESeq2_output/cbaihemat_transcriptomev2.0/amb2_vs_elev2_indiv/AllGenes_wcols.txt",
blast_file = "../data/cbai_hemat_diamond_blastx_table_transcriptome_v2.0.txt",
output_file = "../scripts/16_running_GO-MWU/cbaihemat2.0_amb2_vs_elev2_indiv_pvals.csv")