MissingExons: Find exons for a transcript/gene that are not mapped to the...

In laderast/ExonModelStrain: Strain Specific Exon Modeling

Description

For a given transcript, or gene id, return all Ensembl Exon IDs that do not have mapped probesets.

Usage

  MissingExons(id,ExpSet,dBPackage="mouseexonensembl.db")
  MissingExons(id,ExpSet)

Arguments

id	Valid Ensembl Transcript or Gene ID. Note a list of all valid Transcript or Gene IDs can be queried from the database package by using getAllTranscripts() or getAllGenes().
ExpSet	ExpressionSet containing probeset-level Exon Expression Data. Currently, only Mouse Exon 1.0 data is supported. The ExpressionSet slot phenoData should contain a column called 'Strain' where the two strains are coded 1 and 2.
dbPackage	Name of database package containing Ensembl-Exon Array mapping (currently only mouseexonensembl.db exists).

Details

MissingExons produces a list of Ensembl Exon IDs not mapped to the current Expression Set. This may be for two reasons: either the Exon ID does not have any probesets mapped to it, or these probesets do not exist in the current ExpressionSet (perhaps due to SNP masking, etc).

If all existing Exons are mapped, MissingExons returns a NULL value.

See Also

RunExonModelWorkflow

Examples

  data(exontestdata)
  res <- MissingExons("ENSMUST00000062893",TestSetTrans)
  print(res)

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