Get UniProt Protein Info (GUPPI)

guppi() analyzes a .tdReport file generated by TDPortal or ProSightPD and adds additional data from UniProt.

guppi(
  filedir,
  filename,
  taxonNumber,
  GOLocType = "bacteria",
  fractionAssignments = NULL,
  outputdir,
  fdr = 0.01,
  saveOutput = TRUE,
  makeDashboard = FALSE,

    dashboardPath = glue::glue("{outputdir}/report/{format(Sys.time(), '%Y%m%d_%H%M%S')}_dashboard.html")
)

Arguments

filedir	Character vector of the directory which contains the input file(s). Files can be at any level below the directory, subdirectories are checked recursively.
filename	Character vector of the names of the tdReport files, including extension. Must match the name of the files exactly.
taxonNumber	Numeric vector. NCBI taxon number to be used for getting UniProt data, e.g. 83333 for E. coli K12.
GOLocType	Name of taxon to use for determination of subcellular locations. Acceptable values are "bacteria" and "eukaryota".
fractionAssignments	Optional argument. A named list with names set to the fraction numbers of the input files and values set to the input file names. If left blank, GUPPI will attempt to assign fraction numbers automatically from file names in the tdReport.
outputdir	Character vector. Directory to use for output, files will be saved to subdirectories. Directory will be created if it doesn't exist, as long as parent directory exists.
fdr	False detection rate cutoff for protein and proteoform identifications. Defaults to 0.01 (1%).
saveOutput	Boolean value. Controls whether protein report, proteoform report, etc. are saved to output directory. Doesn't effect GUPPI report. Defaults to TRUE.
makeDashboard	Boolean values. Controls whether GUPPI report is rendered to the output directory. Defaults to FALSE.
dashboardPath	Full path and name of dashboard output (i.e. GUPPI report). Defaults to /report subdirectory of the output directory.

Value

This function is called for its side effects, i.e. the files in the output directory.

Examples

if (FALSE) {
    GUPPI::guppi(
       "C:/Users/David Butcher/TDReports",
       c(
          "20200420_Excellent_TDReport_01.tdReport",
          "20200420_Excellent_TDReport_02.tdReport"
       ),
       83333,
       GOLocType = "bacteria",
       fractionAssignments = NULL,
       outputdir = "C:/Users/David Butcher/guppi_output",
       fdr = 0.01,
       saveOutput = TRUE,
       makeDashboard = TRUE
    )
}