runSIGORA.Rdworkflow for sigORA
runSIGORA( data, target = "GO", score_col = "estimate", ID_col = "UniprotID", threshold = 0.5, outdir = "sigORA", greater = TRUE, myGPSrepo = NULL, DEBUG = FALSE )
| data | data |
|---|---|
| target | target database, default: "GO" |
| score_col | column name containing estimates |
| ID_col | column name containing IDs |
| threshold | threshold for estimate |
| outdir | output directory |
| greater | flag whether to filter > threshold or < threshold |
| myGPSrepo | gps repository |
| DEBUG | default FALSE, if TRUE, skip markdown generation |
library(prora) fc_estimates <- prora::exampleContrastData filtered_dd <- get_UniprotID_from_fasta_header(fc_estimates, idcolumn = "protein_Id") myGPSrepo <- makeGPS_wrappR(filtered_dd$UniprotID, target = "GO") #> 'select()' returned 1:many mapping between keys and columns #> 'select()' returned 1:1 mapping between keys and columns #> Joining, by = "pathwayID" #> Time difference of 1.475307 mins #> Time difference of 1.486356 mins #> Time difference of 1.494625 mins #> Time difference of 1.502429 mins #> Time difference of 1.509996 mins #usethis::use_data(myGPSrepo,overwrite = TRUE) undebug(runSIGORA) #> Warning: argument is not being debugged undebug(sigoraWrappR) #> Warning: argument is not being debugged res <- runSIGORA(filtered_dd, myGPSrepo = prora::myGPSrepo, DEBUG=TRUE) #> pathwy.id description pvalues Bonferroni successes PathwaySize N #> 1 GO:0016021 <NA> 1.240e-191 1.304e-188 871.43 2932.08 124148.2 #> 2 GO:0005789 <NA> 2.573e-61 2.707e-58 343.96 1297.50 124148.2 #> 3 GO:0005874 <NA> 3.292e-33 3.463e-30 121.24 359.39 124148.2 #> 4 GO:0045296 <NA> 5.084e-30 5.348e-27 328.45 1680.28 124148.2 #> 5 GO:0005524 <NA> 2.569e-28 2.703e-25 1540.70 11535.35 124148.2 #> 6 GO:0016032 <NA> 4.736e-28 4.982e-25 205.56 895.53 124148.2 #> 7 GO:0005794 <NA> 4.773e-27 5.021e-24 395.42 2228.09 124148.2 #> 8 GO:0017101 <NA> 6.774e-18 7.126e-15 28.00 42.75 124148.2 #> 9 GO:0051301 <NA> 1.010e-16 1.063e-13 150.55 726.48 124148.2 #> 10 GO:0075733 <NA> 1.441e-14 1.516e-11 96.00 411.00 124148.2 #> 11 GO:0035579 <NA> 1.296e-13 1.363e-10 42.82 117.49 124148.2 #> 12 GO:0004386 <NA> 3.497e-12 3.679e-09 77.50 326.67 124148.2 #> 13 GO:0004725 <NA> 1.774e-11 1.866e-08 45.00 148.75 124148.2 #> 14 GO:0000139 <NA> 3.781e-10 3.978e-07 110.84 583.59 124148.2 #> 15 GO:0019083 <NA> 1.440e-09 1.515e-06 28.07 78.13 124148.2 #> 16 GO:0005768 <NA> 1.585e-09 1.667e-06 32.08 97.61 124148.2 #> 17 GO:0005635 <NA> 3.017e-09 3.174e-06 35.25 116.28 124148.2 #> 18 GO:0016887 <NA> 1.178e-08 1.239e-05 22.51 56.43 124148.2 #> 19 GO:0005516 <NA> 4.120e-07 4.334e-04 25.47 82.47 124148.2 #> 20 GO:0005783 <NA> 6.539e-07 6.879e-04 325.92 2431.01 124148.2 #> 21 GO:0005743 <NA> 6.682e-07 7.029e-04 62.19 318.49 124148.2 #> 22 GO:0005925 <NA> 6.728e-06 7.078e-03 186.77 1317.87 124148.2 #> 23 GO:0006890 <NA> 8.965e-06 9.431e-03 14.93 36.54 124148.2 #> sample.size #> 1 12768.47 #> 2 12768.47 #> 3 12768.47 #> 4 12768.47 #> 5 12768.47 #> 6 12768.47 #> 7 12768.47 #> 8 12768.47 #> 9 12768.47 #> 10 12768.47 #> 11 12768.47 #> 12 12768.47 #> 13 12768.47 #> 14 12768.47 #> 15 12768.47 #> 16 12768.47 #> 17 12768.47 #> 18 12768.47 #> 19 12768.47 #> 20 12768.47 #> 21 12768.47 #> 22 12768.47 #> 23 12768.47 if (FALSE) { rmarkdown::render(res$rmarkdownPath, bookdown::html_document2(number_sections = FALSE), params = res$sigoraData, clean = TRUE) }