annotatePreCalculatedGRs: Create a GRList with a reference GR and a sample GR annotated...
In lldelisle/analysePeaks: Compare, annotate your peaks

Description Usage Arguments Details Value

Create a GRList with a reference GR and a sample GR annotated with GRanges provided in arguments.

annotatePreCalculatedGRs(
  grSetRep,
  grRef,
  myRefLabel,
  stringSet,
  grLScores = NULL,
  grLDistance = NULL,
  useSummitPMFlanking = T,
  flankingSize = 150
)

`grSetRep`	a GenomicRange with the merged replicates to annotate
`grRef`	a GenomicRange with the (merged) reference to annotate
`myRefLabel`	the name to give to the ref
`stringSet`	the name to give to the set
`grLScores`	a GRangeList with annotations for which you would like to know the best score overlapping the GRanges of experiments
`grLDistance`	a GRangeList with annotations for which you would like to know the distance to the closest item
`useSummitPMFlanking`	logical value to specify if you prefer to use the full region of the peak or only the summit +/- the 'flankingSize'
`flankingSize`	integer value used to extend the summit if 'useSummitPMFlanking' is TRUE

The GRanges of myGRs will have in mcols a new information which is bestNameOfTheGRScore for each GR in grLScores and distanceToTheNearestNameOfTheGR for each GR in grLDistance

A list with: 'stringSet' a string with all samples other than the reference separated by comma 'myGRs' a GRangeList of 2 elements which are 1. The peaks which are shared by all samples of mySet 2. The peaks which are shared by all samples of myRef 'nameOfRef' the name of the reference(s) used 'namesOfGrLScores' the names of grLScores 'namesOfGrLDistance' the names of grLDistance 'useSummitPMFlanking' the value of useSummitPMFlanking which was used 'flankingSize' the value of flankingSize which was used

lldelisle/analysePeaks documentation built on July 10, 2021, 1:02 p.m.