viewGRangesWinSample_dt: get a windowed sampling of score_gr

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

get a windowed sampling of score_gr

Description

This method is appropriate when all GRanges in qgr are identical width and when it is practical to use a window_size smaller than features in genomic signal. For instance, when retrieving signal around peaks or promoters this method maintains a fixed genomic scale across regions. This allows meaingful comparison of peak widths can be made.

Usage

viewGRangesWinSample_dt(
  score_gr,
  qgr,
  window_size,
  attrib_var = "score",
  fill_value = 0,
  anchor = c("center", "center_unstranded", "left", "left_unstranded")[1]
)

Arguments

score_gr	GRanges with a "score" metadata column.
qgr	regions to view by window.
window_size	qgr will be represented by value from score_gr every window_size bp.
attrib_var	character name of attribute to pull data from. Default is "score", compatible with with bigWigs or bam coverage.
fill_value	numeric or character value to use where queried regions are empty. Default is 0 and appropriate for both calculated coverage and bedgraph/bigwig like files. Will automatically switch to "MISSING" if data is guessed to be qualitative.
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 "center".

Details

Summarizes score_gr by grabbing value of "score" every window_size bp. 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

data(CTCF_in_10a_overlaps_gr)
bam_file = system.file("extdata/test.bam",
    package = "seqsetvis")
qgr = CTCF_in_10a_overlaps_gr[seq_len(5)]
qgr = GenomicRanges::resize(qgr, width = 500, fix = "center")
bam_gr = seqsetvis:::fetchBam(bam_file, qgr)
bam_dt = viewGRangesWinSample_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 = viewGRangesWinSample_dt(bw_gr, qgr, 50)
}

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.