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Fast Gene Set Enrichment Analysis (FGSEA)

AT Alexis M. Thornton
LF Lishan Fang
AL April Lo
MM Maria McSharry
DH David Haan
CO Casey O’Brien
AB Alice H. Berger
MG Marios Giannakis
AB Angela N. Brooks
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Fast Gene Set Enrichment Analysis (FGSEA) is an R tool that performs preranked gene set enrichment analysis. FGSEA requires a pre-ranked file gene file, that we created from DESeq2’s Wald statistic in two comparisons: (1)GFP vs RNF43 G659fs and (2)RNF43 WT vs RNF43 G659fs. We evaluated the (1)“fgsea” and (2)“fgseaMultilevel” functions and ranked gene input of (1) all genes and (2) mutation-specific genes. Pathways with an adjusted p-value under 0.05 were considered significant. The results for the 8 runs of FGSEA are available in S13 File.

Copyright and License information:  ©2021 Thornton et al
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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