R: This function is the primary function that calls other...

InflectSSP

R Documentation

This function is the primary function that calls other functions in the program.

Description

This function is the primary function that calls other functions in the program.

Usage

InflectSSP(
  Directory,
  NControl,
  NCondition,
  PSM,
  UP,
  CurveRsq,
  PValMelt,
  PValMeltFDR,
  MeltLimit,
  RunSTRING,
  STRINGScore,
  RunPANTHER,
  Species,
  PANTHERpvalue
)

Arguments

`Directory`	the directory where the source data files to be analyzed are saved. This is also the location where the results will be saved.
`NControl`	the number of Control replicate experiments that are to be analyzed
`NCondition`	the number of Condition replicate experiments that are to be analyzed
`PSM`	the number of peptide spectrum matches that are deemed acceptable for reporting
`UP`	the number of unique peptides for a protein that are deemed acceptable for reporting
`CurveRsq`	Coefficient of determination criteria for melt curves
`PValMelt`	p-value criteria for melt shifts
`PValMeltFDR`	Whether or not the FDR correction for pvalue is used in designation of melts of interest
`MeltLimit`	the melt shift temperature limit used for determining which proteins to report as significant
`RunSTRING`	whether or not the STRING function will be run or not in the analysis
`STRINGScore`	the score to be used in the STRING analysis
`RunPANTHER`	whether or not the PANTHER function will be run or not in the analysis
`Species`	species number for bioinformatics search
`PANTHERpvalue`	p-value for PANTHER analysis

Value

the proteins that have significant melt shifts from an experiment

Examples

## Not run: 
     Directory<-'/Users/Einstein'
     NControl<-2
     NCondition<-3
     PSM<-2
     UP<-3
     CurveRsq<-.95
     PValMelt<-0.05
     PValMeltFDR<-"No"
     MeltLimit<-3
     RunSTRING<-"Yes"
     STRINGScore<-0.99
     RunPANTHER<-"Yes"
     Species<-9606
     PANTHERpvalue<-0.05
     InflectSSP(Directory,NControl,
     NCondition,PSM,UP,CurveRsq,PValMelt,PValMeltFDR,
     MeltLimit,RunSTRING,STRINGScore,RunPANTHER,
     Species,PANTHERpvalue)
     
## End(Not run)