validProbeAnno: Function to check a probeAnno environment
In Ringo: R Investigation of ChIP-chip Oligoarrays

Description Usage Arguments Details Value Author(s) See Also Examples

This function checks whether a probeAnno environment seems to be valid and will work with other Ringo functions.

1	validProbeAnno(probeAnno)

probeAnno

an environment that holds probe matches to genomic coordinates

This function checks certain properties of the mapping environment that are used by other Ringo functions. It can indicate potential problems in the environment.

TRUE if the environment seems to be a valid probeAnno environment, FALSE if a potential problems with this environment was identified. This potential problem is explained as a warning.

Joern Toedling

posToProbeAnno

 ## first a toy example:
 if (interactive()){
  A = new.env()
  assign("1.+.start",seq(100,1000,by=100),env=A)
  validProbeAnno(A)
  assign("1.+.end",c(99,seq(250,1050,by=100)),env=A)
  assign("1.+.unique",numeric(10),env=A)
  assign("1.+.index",c(2:5,1,7,8,6,10), env=A)
  validProbeAnno(A)
  assign("1.+.index",c(2:5,1,7,8,6,10,3), env=A)
  validProbeAnno(A)
  assign("1.+.end",c(150,seq(250,1050,by=100)),env=A)
  validProbeAnno(A)
 } 
 ## validate the provided example probeAnno
 load(file.path(system.file("exData",package="Ringo"),"exampleProbeAnno.rda"))
 validProbeAnno(exProbeAnno)