viewGRangesWinSample_dt {seqsetvis} | R Documentation |
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.
viewGRangesWinSample_dt( score_gr, qgr, window_size, attrib_var = "score", fill_value = 0, anchor = c("center", "center_unstranded", "left", "left_unstranded")[1] )
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". |
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.
data.table that is GRanges compatible
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) }