GO enrichment of all genes obtained¶
We use GO_enrichment_FDR.R which allows us to choose between multiple procedures for multiple testing correction. Here we are interested in controlling the FDR ; we can use either pAdjustMethod = "BH" (Benjamini-Hochberg, default parameter) or pAdjustMethod = "fdr".
All results (list of genes and detailed GO enrichment) can be found in main repository in docs/data_and_resuls/haemochromatosis/networks_hemochromatosis.
Dependencies¶
We use R 4.0. We need the clusterProfiler package. See custom_go.md for installation details.
Main remarks¶
- From time to time, one may get the following error while using
GO_enrichment_FDR.R:
Error in `[.data.frame`(d, , 2) : undefined columns selected
This is expected, and should be considered as a warning only (I did not take the time to handle the case with an exception). This happens when no significant GO terms are found ; in such case, no graphical outputs are computed.
Collecting the list of genes of interest¶
cd /work2/project/regenet/workspace/thoellinger/shared/2022/networks_hemochromatosis
We obtained this list using our R markdown doing network analysis of E-G pairs starting from genes directly involved in hemochromatosis or involved in the regulation of iron metabolism.
We saved this list of 457 (13 known + 444 inferred) genes as new_genes_v7.list. For each one of the 13 initial genes, we also saved separately the corresponding inferred genes:
└── results ... ├── new_genes_v7.list # 457 └── separate ├── BMP6.list # 17 ├── CIAPIN1.list # 56 ├── CYBRD1.list # 35 ├── HAMP.list # 35 ├── HFE2.list # 27 ├── HFE.list # 61 ├── NEO1.list # 39 ├── SLC11A2.list # 68 ├── SLC39A14.list # 35 ├── SLC40A1.list # 26 ├── TFR2.list # 34 ├── TFRC.list # 10 └── TMPRSS6.list # 14
GO enrichment¶
module load system/R-4.0.4_gcc-9.3.0
All 457 genes (original + inferred)¶
mkdir -p GO_FDR/all_genes/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/new_genes_v7.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/all_genes/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "457 provided genes; 336 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 3457 distinct GO terms" [1] "Of those 3457 GO terms, 29 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
All 444 genes (inferred only ; w/o original genes)¶
mkdir -p GO_FDR/all_genes_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/new_genes_v7_without_original.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/all_genes_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "444 provided genes; 324 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 3297 distinct GO terms" [1] "Of those 3297 GO terms, 23 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
All genes co-expressed in liver¶
mkdir -p GO_FDR/genes_inferred_from_that_expressed_in_liver/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/genes_inferred_from_that_expressed_in_liver.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/genes_inferred_from_that_expressed_in_liver/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "167 provided genes; 110 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 1595 distinct GO terms" [1] "Of those 1595 GO terms, 0 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
No significant enrichment found in any GO term.
All genes co-expressed in intestine¶
mkdir -p GO_FDR/genes_inferred_from_that_expressed_in_intestine/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/genes_inferred_from_that_expressed_in_intestine.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/genes_inferred_from_that_expressed_in_intestine/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "126 provided genes; 97 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 1522 distinct GO terms" [1] "Of those 1522 GO terms, 6 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Each original gene separately¶
Inferred from BMP6¶
mkdir -p GO_FDR/separate/BMP6/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/BMP6.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/BMP6/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "17 provided genes; 12 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 420 distinct GO terms" [1] "Of those 420 GO terms, 151 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Note that we tried at a more stringent fdr (-f 0.05), and it yielded no significant results ; so we kept the default 0.1 threshold for this one, and a few other ones later.
Inferred from BMP6 w/o BMP6¶
mkdir -p GO_FDR/separate/BMP6_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/BMP6_wo_original.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/BMP6_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "16 provided genes; 11 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 242 distinct GO terms" [1] "Of those 242 GO terms, 108 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from CIAPIN1¶
mkdir -p GO_FDR/separate/CIAPIN1/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/CIAPIN1.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/CIAPIN1/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "56 provided genes; 48 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 1141 distinct GO terms" [1] "Of those 1141 GO terms, 23 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from CIAPIN1 w/o CIAPIN1¶
mkdir -p GO_FDR/separate/CIAPIN1_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/CIAPIN1_wo_original.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/CIAPIN1_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "55 provided genes; 47 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 1138 distinct GO terms" [1] "Of those 1138 GO terms, 23 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from CYBRD1¶
mkdir -p GO_FDR/separate/CYBRD1/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/CYBRD1.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/CYBRD1/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "35 provided genes; 26 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 471 distinct GO terms" [1] "Of those 471 GO terms, 16 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from CYBRD1 w/o CYBRD1¶
mkdir -p GO_FDR/separate/CYBRD1_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/CYBRD1_wo_original.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/CYBRD1_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "34 provided genes; 25 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 466 distinct GO terms" [1] "Of those 466 GO terms, 17 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from HAMP¶
mkdir -p GO_FDR/separate/HAMP/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/HAMP.list -f 0.2 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/HAMP/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "35 provided genes; 28 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 693 distinct GO terms" [1] "Of those 693 GO terms, 0 have a BH-adjusted p-val < 0.2" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
No significant enrichment found in any GO term.
Inferred from HAMP w/o HAMP¶
mkdir -p GO_FDR/separate/HAMP_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/HAMP_wo_original.list -f 0.2 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/HAMP_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "34 provided genes; 27 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 591 distinct GO terms" [1] "Of those 591 GO terms, 0 have a BH-adjusted p-val < 0.2" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
No significant enrichment found in any GO term.
Inferred from HFE2¶
mkdir -p GO_FDR/separate/HFE2/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/HFE2.list -f 0.2 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/HFE2/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "27 provided genes; 19 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 313 distinct GO terms" [1] "Of those 313 GO terms, 2 have a BH-adjusted p-val < 0.2" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
Significant enrichment found for only 2 GO terms. Not sure why it was not enough to compute graphical outputs...? Anyways, output tables we successfully computed.
Inferred from HFE2 w/o HFE2¶
mkdir -p GO_FDR/separate/HFE2_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/HFE2_wo_original.list -f 0.2 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/HFE2_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "26 provided genes; 19 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 313 distinct GO terms" [1] "Of those 313 GO terms, 2 have a BH-adjusted p-val < 0.2" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
Significant enrichment found for only 2 GO terms. Not sure why it was not enough to compute graphical outputs...? Anyways, output tables we successfully computed.
Inferred from NEO1¶
mkdir -p GO_FDR/separate/NEO1/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/NEO1.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/NEO1/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "39 provided genes; 31 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 942 distinct GO terms" [1] "Of those 942 GO terms, 0 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
No significant enrichment found in any GO term.
Inferred from NEO1 w/o NEO1¶
mkdir -p GO_FDR/separate/NEO1_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/NEO1_wo_original.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/NEO1_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "38 provided genes; 30 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 933 distinct GO terms" [1] "Of those 933 GO terms, 0 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
No significant enrichment found in any GO term.
Inferred from SLC11A2¶
mkdir -p GO_FDR/separate/SLC11A2/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/SLC11A2.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/SLC11A2/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "68 provided genes; 55 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 1022 distinct GO terms" [1] "Of those 1022 GO terms, 7 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from SLC11A2 w/o SLC11A2¶
mkdir -p GO_FDR/separate/SLC11A2_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/SLC11A2_wo_original.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/SLC11A2_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "67 provided genes; 54 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 998 distinct GO terms" [1] "Of those 998 GO terms, 7 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." ... [1] "Done."
Inferred from SLC39A14¶
mkdir -p GO_FDR/separate/SLC39A14/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/SLC39A14.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/SLC11A2/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "35 provided genes; 26 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 584 distinct GO terms" [1] "Of those 584 GO terms, 3 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from SLC39A14 w/o SLC39A14¶
mkdir -p GO_FDR/separate/SLC39A14_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/SLC39A14_wo_original.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/SLC11A2_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "34 provided genes; 25 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 541 distinct GO terms" [1] "Of those 541 GO terms, 2 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from SLC40A1¶
mkdir -p GO_FDR/separate/SLC40A1/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/SLC40A1.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/SLC40A1/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "26 provided genes; 19 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 401 distinct GO terms" [1] "Of those 401 GO terms, 2 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from SLC40A1 w/o SLC40A1¶
mkdir -p GO_FDR/separate/SLC40A1_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/SLC40A1_wo_original.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/SLC40A1_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "25 provided genes; 18 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 381 distinct GO terms" [1] "Of those 381 GO terms, 2 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from TFR2¶
mkdir -p GO_FDR/separate/TFR2/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/TFR2.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/TFR2/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "34 provided genes; 27 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 386 distinct GO terms" [1] "Of those 386 GO terms, 0 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
No significant enrichment found in any GO term.
Inferred from TFR2 w/o TFR2¶
mkdir -p GO_FDR/separate/TFR2_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/TFR2_wo_original.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/TFR2_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "33 provided genes; 26 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 360 distinct GO terms" [1] "Of those 360 GO terms, 0 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." Error in `[.data.frame`(d, , 2) : undefined columns selected Calls: upsetplot ... eval_tidy -> split -> split.default -> [ -> [.data.frame Execution halted
No significant enrichment found in any GO term.
Inferred from TFRC¶
mkdir -p GO_FDR/separate/TFRC/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/TFRC.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/TFRC/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "10 provided genes; 5 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 172 distinct GO terms" [1] "Of those 172 GO terms, 141 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from TFRC w/o TFRC¶
mkdir -p GO_FDR/separate/TFRC_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/TFRC_wo_original.list -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/TFRC_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "9 provided genes; 4 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 66 distinct GO terms" [1] "Of those 66 GO terms, 66 have a BH-adjusted p-val < 0.1" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from TMPRSS6¶
mkdir -p GO_FDR/separate/TMPRSS6/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/TMPRSS6.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/TMPRSS6/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "14 provided genes; 13 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 257 distinct GO terms" [1] "Of those 257 GO terms, 8 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
Inferred from TMPRSS6 w/o TMPRSS6¶
mkdir -p GO_FDR/separate/TMPRSS6_wo_orig/symbol
Rscript GO_enrichment_FDR.R -k "SYMBOL" -G results/separate/TMPRSS6_wo_original.list -f 0.05 -c "BP" -a "BH" -o "default_universe" -d "GO_FDR/separate/TMPRSS6_wo_orig/symbol"
... [1] "Loading input data..." [1] "Warning: using defaut universe automatically provided by the clusterProfiler package" [1] "Done." [1] "Computing GO enrichment..." `universe` is not in character and will be ignored... [1] "Done." [1] "18866 (default) background genes" [1] "13 provided genes; 12 found by `enrichGO`" [1] "Computed GO enrichment (whether significant or not) for 237 distinct GO terms" [1] "Of those 237 GO terms, 10 have a BH-adjusted p-val < 0.05" [1] "Writing outputs tables..." [1] "Done. Writing output images..." ... [1] "Done."
