Find non-zero regions in a Rle

Find genomic regions for which a numeric vector is above (or below) predefined thresholds. In other words, this function finds the candidate Differentially Expressed Regions (candidate DERs). This is similar to regionFinder and is a helper function for calculatePvalues.

findRegions(
  position = NULL,
  fstats,
  chr,
  oneTable = TRUE,
  maxClusterGap = 300L,
  cutoff = quantile(fstats, 0.99, na.rm = TRUE),
  segmentIR = NULL,
  smooth = FALSE,
  weights = NULL,
  smoothFunction = bumphunter::locfitByCluster,
  ...
)

Arguments

position

A logical Rle of genomic positions. This is generated in loadCoverage. Note that it gets updated in preprocessCoverage if colsubset is not NULL.

fstats

A numeric Rle with the F-statistics. Usually obtained using calculateStats.

chr

A single element character vector specifying the chromosome name.

oneTable

If TRUE only one GRanges is returned. Otherwise, a GRangesList with two components is returned: one for the regions with positive values and one for the negative values.

maxClusterGap

This determines the maximum gap between candidate DERs. It should be greater than maxRegionGap (0 by default).

cutoff

Threshold applied to the fstats used to determine the regions.

segmentIR

An IRanges object with the genomic positions that are potentials DERs. This is used in calculatePvalues to speed up permutation calculations.

smooth

Whether to smooth the F-statistics (fstats) or not. This is by default FALSE. For RNA-seq data we recommend using FALSE.

weights

Weights used by the smoother as described in smoother.

smoothFunction

A function to be used for smoothing the F-statistics. Two functions are provided by the bumphunter package: loessByCluster and runmedByCluster. If you are using your own custom function, it has to return a named list with an element called $fitted that contains the smoothed F-statistics and an element claled $smoothed that is a logical vector indicating whether the F-statistics were smoothed or not. If they are not smoothed, the original values will be used.

...

Arguments passed to other methods and/or advanced arguments. Advanced arguments:

verbose: If TRUE basic status updates will be printed along the way.
basic: If TRUE a DataFrame is returned that has only basic information on the candidate DERs. This is used in calculatePvalues to speed up permutation calculations. Default: FALSE.
maxRegionGap: This determines the maximum number of gaps between two genomic positions to be considered part of the same candidate region. The default is 0L.

Passed to extendedMapSeqlevels and the internal function .getSegmentsRle that has by default verbose = FALSE.

When smooth = TRUE, ... is passed to the internal function .smootherFstats. This internal function has the advanced argument maxClusterGap (same as above) and passes ... to define_cluster and the formal arguments of smoothFun.

Value

Either a GRanges or a GRangesList as determined by oneTable. Each of them has the following metadata variables.

value: The mean of the values of y for the given region.
area: The absolute value of the sum of the values of y for the given region.
indexStart: The start position of the region in terms of the index for y.
indexEnd: The end position of the region in terms of the index for y.
cluster: The cluser ID.
clusterL: The total length of the cluster.

Details

regionFinder adapted to Rle world.

References

Rafael A. Irizarry, Martin Aryee, Hector Corrada Bravo, Kasper D. Hansen and Harris A. Jaffee. bumphunter: Bump Hunter. R package version 1.1.10.

Author

Leonardo Collado-Torres

Examples