createMyGRsUsingSimpleOverlap: 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 not a one-to-one match between the Set and the Reference but just an overlap.

createMyGRsUsingSimpleOverlap(
  mySet,
  allExpe,
  ovCluster = NULL,
  grLScores = NULL,
  grLDistance = NULL,
  myRef = c("ChIP"),
  useSummitPMFlanking = T,
  flankingSize = 150
)

`mySet`	a vector with the name of the samples to compare to the ref
`allExpe`	a GRangeList with at least each sample in 'mySet' and 'myRef'
`ovCluster`	a dataframe summurizing the cluster by overlap if previously calculated (default is NULL)
`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
`myRef`	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 have the coordinates of the first item of 'mySet' and will also have inNoneOfTheRef. The second item of myGRs have the coordinates of the first item of 'myRef' and will also have inNoneOfTheSet. Every overlap was considered and used to make "cluster", only the peak with the higest score whithin the same cluster is used in the output.

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 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.