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README_find_enrichment.md

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Gene Ontolog Enrichment Analyses (GOEA) from the command-line

Run GOEA and print GO terms

  1. with uncorrected pvalues < 0.05 to the screen: (default)
  2. with uncorrected pvalues < 0.05 to the screen, grouped: --sections=...
  3. with uncorrected pvalues < 0.05 to files: --outfile=goea.xlsx
  4. with Benjamini-Hochberg pvalues < 0.05 (plus bonferroni, sidak, holm) --pval_field=fdr_bh
  5. with Benjamini-Hochberg pvalues < 0.05 to an xlsx file
    --method=fdr_bh --outfile=goea_fdr_bh_flat.xlsx
  6. with Benjamini-Hochberg pvalues < 0.05 to an xlsx file, grouped
    --method=fdr_bh --outfile=goea_fdr_bh_grpd.xlsx --sections...
  7. regardless of pvalue (ALL GO terms) --pval=-1

Example Details

CMD: python scripts/find_enrichment.py data/study data/population data/association --outfile=goea.xlsx,goea.tsv --pval_field=fdr_bh

1) Print GO terms with uncorrected pvalues < 0.05 to the screen (default)

The default is to print all GO terms with uncorrected P-values < 0.05 (default)

python scripts/find_enrichment.py data/study data/population data/association
GO NS ep name study pop p_uncorrected depth # study p_bonferroni p_sidak p_holm p_fdr_bh study_items
GO:0036211 BP e protein modification process 33/276 1725/33239 8.07048771243e-06 5 33 0.0491331291933 0.0478945023525 0.0491089177301 0.00982662583865 AT1G13580...
GO:0006464 BP e cellular protein modification process 33/276 1725/33239 8.07048771243e-06 6 33 0.0491331291933 0.0478945023525 0.0491089177301 0.00982662583865 AT1G13580...

2) Print GO terms with uncorrected pvalues < 0.05 to the screen, grouped

optional attribute: --sections=goatools.test_data.sections.data2018_07_find_enrichment

Acceptable values for --sections are:

File type Example value
Python module goatools.test_data.sections.data2018_07_find_enrichment
text file sections.txt
Python file goatools/test_data/sections/data2018_07_find_enrichment.py 
python scripts/find_enrichment.py data/study data/population data/association --sections=goatools.test_data.sections.data2018_07_find_enrichment

protein
GO:0036211 BP e 9.83e-03  1320  5.14 D05  33/276  1725/33239 protein modification process ...
GO:0006464 BP e 9.83e-03  1318  5.14 D06  33/276  1725/33239 cellular protein modification process ...
...

phosph
GO:0016301 MF e 4.64e-02   355  4.87 D04  25/276  1310/33239 kinase activity ...
...

3) Print GO terms with uncorrected pvalues < 0.05 to an xlsx file

optional attribute: --outfile=goea_uncorr.xlsx

$ python scripts/find_enrichment.py data/study data/population data/association --outfile=goea_uncorr.xlsx
    ...
    253 items WROTE: goea.xlsx

4) Print GO terms with Benjamini-Hochberg pvalues < 0.05

optional attribute: --pval_field=fdr_bh
optional attribute: ----outfile=goea_fdr_bh.xlsx,goea_fdr_bh.tsv

$ python scripts/find_enrichment.py data/study data/population data/association --outfile=goea_fdr_bh.xlsx,goea_fdr_bh.tsv --pval_field=fdr_bh
     17 items WROTE: goea.xlsx
     17 items WROTE: goea.tsv

5) Print GO terms with Benjamini-Hochberg (only) pvalues < 0.05 to an xlsx file

optional attribute: --method=fdr_bh
optional attribute: --outfile=goea_fdr_bh_flat.xlsx

$ python scripts/find_enrichment.py data/study data/population data/association --outfile=goea_fdr_bh_flat.xlsx --method=fdr_bh
     17 items WROTE: goea_fdr_bh_flat.xlsx

6) Print GO terms with Benjamini-Hochberg (only) pvalues < 0.05 to an xlsx file, grouped

optional attribute: --method=fdr_bh
optional attribute: --outfile=goea_fdr_bh_grpd.xlsx
optional attribute: --sections=goatools.test_data.sections.data2018_07_find_enrichment

$ python scripts/find_enrichment.py data/study data/population data/association --outfile=goea_fdr_bh_grpd.xlsx --method=fdr_bh --sections=goatools.test_data.sections.data2018_07_find_enrichment
     17 items WROTE: goea_fdr_bh_grpd.xlsx

7) Print all GO terms, regardless of pvalue

optional attribute: --pval=-1

$ python scripts/find_enrichment.py data/study data/population data/association --outfile=goea_all.xlsx,goea_all.tsv --pval=-1
   6088 items WROTE: goea.xlsx
   6088 items WROTE: goea.tsv

Copyright (C) 2010-2018, DV Klopfenstein, Haibao Tang, et al. All rights reserved.