getMaxPositionsBySignal: Find sites with max signal in regions of interest
In BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data

Description Usage Arguments Value Author(s) See Also Examples

For each signal-containing region of interest, find the single site with the most signal. Sites can be found at base-pair resolution, or defined for larger bins.

getMaxPositionsBySignal(
  dataset.gr,
  regions.gr,
  binsize = 1,
  bin.centers = FALSE,
  field = "score",
  keep.signal = FALSE,
  expand_ranges = FALSE
)

`dataset.gr`	A GRanges object in which signal is contained in metadata (typically in the "score" field).
`regions.gr`	A GRanges object containing regions of interest.
`binsize`	The size of bin in which to calculate signal scores.
`bin.centers`	Logical indicating if the centers of bins are returned, as opposed to the entire bin. By default, entire bins are returned.
`field`	The metadata field of `dataset.gr` to be counted.
`keep.signal`	Logical indicating if the signal value at the max site should be reported. If set to `TRUE`, the values are kept as a new `MaxSiteSignal` metadata column in the output GRanges.
`expand_ranges`	Logical indicating if ranges in `dataset.gr` should be treated as descriptions of single molecules (`FALSE`), or if ranges should be treated as representing multiple adjacent positions with the same signal (`TRUE`). See `getCountsByRegions`.

Output is a GRanges object with regions.gr metadata, but each range only contains the site within each regions.gr range that had the most signal. If binsize > 1, the entire bin is returned, unless bin.centers = TRUE, in which case a single-base site is returned. The site is set to the center of the bin, and if the binsize is even, the site is rounded to be closer to the beginning of the range.

The output may not be the same length as regions.gr, as regions without signal are not returned. If no regions have signal (e.g. as could happen if running this function on single regions), the function will return an empty GRanges object with intact metadata columns.

If keep.signal = TRUE, the output will also contain metadata for the signal at the max site, named MaxSiteSignal.

Mike DeBerardine

getCountsByPositions

data("PROseq") # load included PROseq data
data("txs_dm6_chr4") # load included transcripts

#--------------------------------------------------#
# first 50 bases of transcripts
#--------------------------------------------------#

pr <- promoters(txs_dm6_chr4, 0, 50)
pr[1:3]

#--------------------------------------------------#
# max sites
#--------------------------------------------------#

getMaxPositionsBySignal(PROseq, pr[1:3], keep.signal = TRUE)

#--------------------------------------------------#
# max sites in 5 bp bins
#--------------------------------------------------#

getMaxPositionsBySignal(PROseq, pr[1:3], binsize = 5, keep.signal = TRUE)