sigoraWrappR.RdProvides a wrapper for sigora::sigora() combined with sigora::ora() and
returns a list used for the generation of an .Rmd report.
sigoraWrappR( data, threshold = 0.5, score_col = "", GPSrepos = sigora::load_data("kegH"), db = "", greater_than = TRUE, idmap = sigora::idmap )
| data | input data.frame (at least two columns, first column containing IDs, other columns numerical ranks, i.e. fold changes) |
|---|---|
| threshold | fold change threshold above which (in absolute terms) a protein is considered differentially regulated |
| score_col | Name of the fold change column, in case the input file contains multiple contrasts |
| GPSrepos | GPS repository used as background, can be
generated via |
| db | database used for the generation of the GPS repository |
| greater_than | Logical. Whether fc_threshold should be applied as
greater_than (default is |
| idmap | id mapping table, dafault sigora::idmap |
Returns a list containing the following elements:
sigora: data.frame containing sigora results
ora: data.frame containing ora results
fc_threshold: fc_threshold used
GPS_repository: GPS repository used, to be reported
database: Database used for generating the GPS repository
data: data.frame containing Uniprot IDs and fold changes
proteinsAfterFiltering: numeric, number of proteins after fc filtering
library(prora) df <- get_UniprotID_from_fasta_header(prora::exampleContrastData) myGPSrepo <- makeGPS_wrappR(ids = df$UniprotID,target = "KEGG") #> 'select()' returned 1:many mapping between keys and columns #> Joining, by = "pathwayID" #> Time difference of 0.6526198 secs #> Time difference of 1.136227 secs res <- sigoraWrappR(df,score_col = "estimate", GPSrepos = myGPSrepo$gps, threshold = 0.5) #> pathwy.id description pvalues Bonferroni #> 1 03010 Ribosome 1.143e-221 1.532e-219 #> 2 03060 Protein export 1.008e-15 1.351e-13 #> 3 04141 Protein processing in endoplasmic reticulum 4.155e-10 5.568e-08 #> 4 05160 Hepatitis C 2.422e-08 3.245e-06 #> 5 04144 Endocytosis 2.813e-07 3.769e-05 #> 6 04530 Tight junction 2.479e-06 3.322e-04 #> 7 04510 Focal adhesion 3.521e-06 4.718e-04 #> 8 04114 Oocyte meiosis 3.458e-05 4.634e-03 #> 9 04360 Axon guidance 3.606e-05 4.832e-03 #> successes PathwaySize N sample.size #> 1 654.12 1577.52 27971.51 3192.29 #> 2 39.27 83.71 27971.51 3192.29 #> 3 340.68 2176.34 27971.51 3192.29 #> 4 36.99 119.34 27971.51 3192.29 #> 5 343.99 2334.53 27971.51 3192.29 #> 6 82.61 432.19 27971.51 3192.29 #> 7 37.00 149.14 27971.51 3192.29 #> 8 30.88 122.42 27971.51 3192.29 #> 9 27.62 104.61 27971.51 3192.29 myGPSrepoGO <- makeGPS_wrappR(df$UniprotID, target = "GO") #> 'select()' returned 1:many mapping between keys and columns #> 'select()' returned 1:1 mapping between keys and columns #> Joining, by = "pathwayID" #> Time difference of 1.365996 mins #> Time difference of 1.375544 mins #> Time difference of 1.383482 mins #> Time difference of 1.391702 mins #> Time difference of 1.399664 mins res <- sigoraWrappR(df,score_col = "estimate", GPSrepos = myGPSrepoGO$gps, threshold = 0.5) #> pathwy.id #> 1 GO:0016021 #> 2 GO:0016032 #> 3 GO:0005789 #> 4 GO:0045296 #> 5 GO:0005524 #> 6 GO:0001228 #> 7 GO:0005783 #> 8 GO:0005794 #> 9 GO:0017101 #> 10 GO:0005874 #> 11 GO:0012507 #> 12 GO:0030134 #> 13 GO:0075733 #> 14 GO:0003724 #> 15 GO:0005925 #> 16 GO:0035579 #> 17 GO:0031267 #> 18 GO:0019083 #> 19 GO:0005525 #> 20 GO:0000139 #> 21 GO:0051301 #> 22 GO:0005635 #> 23 GO:0006886 #> 24 GO:0005887 #> 25 GO:0006364 #> 26 GO:0006606 #> description #> 1 integral component of membrane #> 2 viral process #> 3 endoplasmic reticulum membrane #> 4 cadherin binding #> 5 ATP binding #> 6 DNA-binding transcription activator activity, RNA polymerase II-specific #> 7 endoplasmic reticulum #> 8 Golgi apparatus #> 9 aminoacyl-tRNA synthetase multienzyme complex #> 10 microtubule #> 11 ER to Golgi transport vesicle membrane #> 12 COPII-coated ER to Golgi transport vesicle #> 13 intracellular transport of virus #> 14 RNA helicase activity #> 15 focal adhesion #> 16 specific granule membrane #> 17 small GTPase binding #> 18 viral transcription #> 19 GTP binding #> 20 Golgi membrane #> 21 cell division #> 22 nuclear envelope #> 23 intracellular protein transport #> 24 integral component of plasma membrane #> 25 rRNA processing #> 26 protein import into nucleus #> pvalues Bonferroni successes PathwaySize N sample.size #> 1 8.598e-148 9.999e-145 656.83 2263.46 124990.2 12271.49 #> 2 2.663e-44 3.097e-41 279.48 1175.51 124990.2 12271.49 #> 3 1.822e-36 2.119e-33 277.46 1278.58 124990.2 12271.49 #> 4 1.166e-26 1.356e-23 273.11 1430.53 124990.2 12271.49 #> 5 5.901e-25 6.863e-22 1171.51 8971.63 124990.2 12271.49 #> 6 6.090e-23 7.083e-20 82.82 253.93 124990.2 12271.49 #> 7 6.563e-23 7.633e-20 454.78 2921.41 124990.2 12271.49 #> 8 4.686e-21 5.450e-18 355.99 2192.06 124990.2 12271.49 #> 9 1.985e-18 2.309e-15 28.00 42.75 124990.2 12271.49 #> 10 1.225e-16 1.425e-13 70.90 244.62 124990.2 12271.49 #> 11 1.602e-16 1.863e-13 36.37 77.95 124990.2 12271.49 #> 12 6.219e-16 7.233e-13 23.00 33.70 124990.2 12271.49 #> 13 1.713e-15 1.992e-12 88.00 364.76 124990.2 12271.49 #> 14 2.413e-15 2.806e-12 99.38 437.49 124990.2 12271.49 #> 15 5.676e-12 6.601e-09 191.35 1180.57 124990.2 12271.49 #> 16 6.186e-12 7.194e-09 36.13 104.39 124990.2 12271.49 #> 17 1.801e-10 2.095e-07 51.28 200.73 124990.2 12271.49 #> 18 5.015e-10 5.832e-07 28.35 77.76 124990.2 12271.49 #> 19 1.099e-09 1.278e-06 82.01 418.32 124990.2 12271.49 #> 20 2.261e-09 2.630e-06 87.43 459.80 124990.2 12271.49 #> 21 2.722e-09 3.166e-06 98.17 541.65 124990.2 12271.49 #> 22 3.829e-09 4.453e-06 31.61 99.99 124990.2 12271.49 #> 23 1.087e-08 1.264e-05 70.16 353.18 124990.2 12271.49 #> 24 1.583e-08 1.841e-05 30.48 100.32 124990.2 12271.49 #> 25 3.118e-08 3.626e-05 43.21 179.92 124990.2 12271.49 #> 26 6.041e-06 7.026e-03 10.16 20.44 124990.2 12271.49 if (FALSE) { res$ora res$sigora$summary_results res$data GPSrepo <- myGPSrepoGO$gps }