getMaxPositionsBySignal: Find sites with max signal in regions of interest

In mdeber/BRGenomics: Tools for the Efficient Analysis of High-Resolution Genomics Data

Find sites with max signal in regions of interest

Description

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.

Usage

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

Arguments

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.

Value

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.

Author(s)

Mike DeBerardine

See Also

getCountsByPositions

Examples

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)

mdeber/BRGenomics documentation built on Aug. 3, 2024, 3:43 a.m.