createMyGRs: 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. Here this is a one-to-one match between the Set and the Reference.

createMyGRs(
  e,
  ovF,
  allExpe,
  grLScores = NULL,
  grLDistance = NULL,
  nameOfRef = "ChIP",
  useSummitPMFlanking = T,
  flankingSize = 150
)

`e`	name of the experiment usually sample1____sample2(____sample3 etc...)
`ovF`	a list which contains the filtered overlaps between the samples. Should at least contains a item named e.
`allExpe`	a GRangeList with at least each sample in 'e'
`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
`nameOfRef`	among the samples which one is the reference, the others will be merged as "replicates"
`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 The first item of myGRs will also have inUniqueRef which is the index of the merged item of the Reference. The second item of myGRs will also have inNoneOfTheSet

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 which are considered as "replicates" 2. The peaks of the reference 'nameOfRef' the name of the reference 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.