runPonder: PONDER workflow: Run PONDER analysis
In fursham-h/ponder:

Execute core analysis

runPonder(
  prepObject,
  testNMD = TRUE,
  testOtherFeatures = FALSE,
  PTC_dist = 50,
  testAS = FALSE,
  makeGTF = FALSE,
  clusters = 4
)

`prepObject`	S4 object from prepNMDer output
`testNMD`	If TRUE, program will test transcripts for primary NMD feature
`testOtherFeatures`	If TRUE, program will test transcripts for other NMD features
`PTC_dist`	Minimum distance of PTC to last exon-junction to trigger NMD. Default: 50bp
`testAS`	If TRUE, program will test for alternatively spliced segments
`makeGTF`	If TRUE, program will output a GTF file of query Provide path to output
`clusters`	Number of cores to run the program. Default = 4