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2.3. Output Contents (FastDTLgoea)

moshi edited this page Oct 27, 2021 · 7 revisions

Output Contents

In this page, explain output contents of following 3 directories in 04_functional_analysis.

.
├── 00_user_data/  
├── 01_orthofinder/ 
├── 02_dtl_reconciliation/  
├── 03_aggregate_map_result/  
├── 04_functional_analysis/  -- GOEA(GO Enrichment Analysis) result
│   ├── go_annotation/   -- InterProScan GOterm annotation result 
│   ├── go_enrichment/   -- Gain/Loss gene GOEA result
│   └── result_summary/  -- GOEA summary result
└── log/

1. go_annotation/

go_annotation directory contains genomic CDSs InterProScan GOterm annotation files (*.tsv).

See InterProScan document for GOterm annotation file format details.

2. go_enrichment/

go_enrichment directory contains GOEA running work files.
All results are aggregated in result_summary directory.

3. result_summary/

result_summary contains 1 directory and 2 files.

  • significant_go_plot/

    Significant GOterms plot figure files like below.

    demo_plot_goea.png

  • significant_go_count.tsv

    Significant GOterms count file.

    Columns Content
    NODE_ID NODE ID
    GAIN/LOSS "gain" or "loss"
    GO_CATEGORY "BP" or "MF" or "CC"
    OVER/UNDER "over" or "under"
    SIGNIFICANT_GO_COUNT Significant GOterm count
    SIGNIFICANT_GO_LIST Significant GOterm list (e.g. GO:44237|GO:0071704)
  • significant_go_list.tsv

    Significant GOterms list file.

    Columns Content
    NODE_ID NODE ID
    GAIN/LOSS "gain" or "loss"
    GO_CATEGORY "BP" or "MF" or "CC"
    OVER/UNDER "over" or "under"
    GO GOterms ID
    GO_NAME GOterms definition
    RATIO_IN_STUDY Ratio in study (gain or loss)
    RATIO_IN_POP Ratio in population
    PVALUE P-value
    DEPTH GOterm depth
    STUDY_COUNT Study GOterms count
    BH_ADJUSTED_PVALUE Benjamini-Hochberge adjusted P-value
    STUDY_ITEMS Study GOterms list
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