sigoraWrappR: sigora Wrapper function
In protViz/fgcz.gsea.ora: ORA, sigORA and GSEA functionalities for proteomic data

Description Usage Arguments Value Examples

Provides 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 `sigoraWrappR`
`db`	database used for the generation of the GPS repository
`greater_than`	Logical. Whether fc_threshold should be applied as greater_than (default is `TRUE`) or strictly less than (`FALSE`)
`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$UniprotID,target = "KEGG")
res <- sigoraWrappR(df,score_col = "estimate", GPSrepos = myGPSrepo$gps,
                     threshold = 0.5)

myGPSrepoGO <- makeGPS_wrappR(df$UniprotID, target = "GO")
res <- sigoraWrappR(df,score_col = "estimate", GPSrepos = myGPSrepoGO$gps,
                     threshold = 0.5)
## Not run: 
  res$ora
res$sigora$summary_results
res$data
GPSrepo <-  myGPSrepoGO$gps

## End(Not run)