viewGRangesWinSummary_dt {seqsetvis}R Documentation

Summarizes signal in bins. The same number of bins per region in qgr is used and widths can vary in qgr, in contrast to viewGRangesWinSample_dt where width must be constant across regions.

Description

This function is most appropriate where features are expected to vary greatly in size and feature boundaries are important, ie. gene bodies, enhancers or TADs.

Usage

viewGRangesWinSummary_dt(score_gr, qgr, n_tiles = 100, anchor = c("center",
  "center_unstranded", "left", "left_unstranded")[3],
  summary_FUN = stats::weighted.mean)

Arguments

score_gr

GRanges with a "score" metadata column.

qgr

regions to view by window.

n_tiles

numeric >= 1, the number of tiles to use for every region in qgr.

anchor

character. controls how x value is derived from position for each region in qgr. 0 may be the left side or center. If not unstranded, x coordinates are flipped for (-) strand. One of c("center", "center_unstranded", "left", "left_unstranded"). Default is "left".

summary_FUN

function. used to aggregate score by tile. must accept x=score and w=width numeric vectors as only arguments. default is weighted.mean. limma::weighted.median is a good alternative.

Details

Columns in output data.table are: standard GRanges columns: seqnames, start, end, width, strand id - matched to names(score_gr). if names(score_gr) is missing, added as 1:length(score_gr) y - value of score from score_gr x - relative bp position

Value

data.table that is GRanges compatible

Examples

bam_file = system.file("extdata/test.bam",
    package = "seqsetvis")
qgr = CTCF_in_10a_overlaps_gr[1:5]
# unlike viewGRangesWinSample_dt, width is not fixed
# qgr = GenomicRanges::resize(qgr, width = 500, fix = "center")
bam_gr = fetchBam(bam_file, qgr)
bam_dt = viewGRangesWinSummary_dt(bam_gr, qgr, 50)

if(Sys.info()['sysname'] != "Windows"){
    bw_file = system.file("extdata/MCF10A_CTCF_FE_random100.bw",
        package = "seqsetvis")
    bw_gr = rtracklayer::import.bw(bw_file, which = qgr)
    bw_dt = viewGRangesWinSummary_dt(bw_gr, qgr, 50)
}

[Package seqsetvis version 1.0.2 Index]