RunQVals: Run qvalue on a resultframe

In laderast/ExonModelStrain: Strain Specific Exon Modeling

Description

For a resultframe produced by RunExonModelWorkflow, produce a new resultframe containing qvalues (FDR adjusted pvalues).

Usage

  RunQVals(resultframe)

Arguments

resultframe

Valid resultframe (either multi or singles) produced from RunExonModelWorkflow.

Details

RunQVals produces a dataframe that also contains the qvalues.

Note that if qvalue cannot produce qvalues for that set of pvalues, the function will return a column of NAs for that set of pvalues, as well as the warning from qvalues.

See Also

RunExonModelWorkflow qvalue

Examples

  #mouseexonensembl.db package required
  #load in sample dataset
  data(exontestdata)
  #show output of RunExonModelWorkflow
  multi[1:5]
  output <- RunQVals(multi)
  output

  ##not run
  ##usually, would run with the output of RunExonModelWorkflow as below:
  ##results <- RunExonModelWorkflow(TestSetTrans, testTrans, dBPackage="mouseexonensembl.db")
  ##this example will not work - not enough pvalues to build a distribution 
  ##9 out of the 20 transcripts are multiple-exon transcripts
  ##run on trx with multiple exons
  ##mult <- RunQVals(results$multi)
  ##mult
  ##run on trx with single exons
  ##singles <- RunQVals(results$single)
  ##singles

laderast/ExonModelStrain documentation built on May 20, 2019, 7:32 p.m.