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,
      attrib_var = "score", attrib_type = NULL, fill_value = 0,
      anchor = c("center", "center_unstranded", "left",
      "left_unstranded")[1], 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.
`attrib_var` | character name of attribute to pull data from. Default is "score", compatible with with bigWigs or bam coverage.
`attrib_type` | one of NULL, qualitative or quantitative. If NULL will attempt to guess by casting attrib_var attribute to character or factor. Default is NULL.
`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".
`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 = seqsetvis:::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 1.7.5 Index]