Thnanks! It worked!!
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Hi, all!
I've obtained the enriched GO BP terms using fGSEA in R as shown below.
1: GO_POSITIVE_REGULATION_OF_VIRAL_TRANSCRIPTION 0.020378457 0.08797654 0.4748196 1.5113374 13 41 TFAP4,NELFCD,POLR2H,POLR2D,NELFA,DHX9,...
2: GO_CARDIAC_CHAMBER_DEVELOPMENT 0.005847953 0.04827840 -0.3775346 -1.7146207 0 166 TEK,FOXF1,CCM2L,TGFBR3,SLIT3,TGFBR2,...
3: GO_DNA_DEPENDENT_DNA_REPLICATION_MAINTENANCE_OF_FIDELITY 0.001461988 0.04816766 0.6526836 2.0851705 0 42 EME1,DNA2,TIMELESS,BLM,TONSL,RAD51,...
4: GO_CIRCADIAN_RHYTHM 0.626463700 0.79544296 0.2392950 0.9379309 534 194 TOP2A,EZH2,TIMELESS,LGR4,NMU,SUV39H2,...
5: GO_PHOSPHATIDYLSERINE_ACYL_CHAIN_REMODELING 0.488165680 0.69185315 -0.3223920 -0.9673269 164 21 PLA2G4F,PLA2G5,LPCAT3,PLA2G2A,PLA2G1B
6: GO_SPINAL_CORD_DEVELOPMENT 0.334183673 0.55175132 0.2905675 1.0667585 261 104 MNX1,SOX4,HOXC10,SOX11,LHX5,SOX12,...
What I'm troubling is saving the result to a file.
I've tried 'write.csv' and 'write_csv', but both failed because the presence of a list (or lists) in the result that I couldn't see.
> write.csv(fgseaRes,"test.csv")
Error in write.table(fgseaRes, "test.csv", col.names = NA, sep = ",", :
unimplemented type 'list' in 'EncodeElement'
> write_csv(fgseaRes,"test.csv")
Error in stream_delim_(df, path, ..., bom = bom, quote_escape = quote_escape) :
Don't know how to handle vector of type list.
Anyone knows how to save this to txt or csv files?
Thank you!
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Hi, have you tried to change your data type ? With functions like
base::as.data.frame()?