ssvFetchBam {seqsetvis} | R Documentation

## Iterates a character vector (ideally named) and calls `ssvFetchBam.single` on each. Appends grouping variable to each resulting data.table and uses rbindlist to efficiently combine results

### Description

`ssvFetchBam` iteratively calls `fetchWindowedBam.single`. See `ssvFetchBam.single` for more info.

### Usage

    ssvFetchBam(file_paths, qgr, unique_names = names(file_paths),
      win_size = 50, win_method = c("sample", "summary")[1],
      summary_FUN = stats::weighted.mean, fragLens = "auto",
      target_strand = c("*", "+", "-")[1], anchor = c("left", "left_unstranded",
      "center", "center_unstranded")[3], names_variable = "sample",
      return_data.table = FALSE)

### Arguments

`file_paths` | The character vector or list of paths to bigwig files to read from.
`qgr` | Set of GRanges to query. For valid results the width of each interval should be identical and evenly divisible by `win_size`.
`unique_names` | names to use in final data.table to designate source bigwig. Default is 'sample'
`win_size` | The window size that evenly divides widths in `qgr`.
`win_method` | character. one of c("sample", "summary"). Determines if `viewGRangesWinSample_dt` or `viewGRangesWinSummary_dt` is used to represent each region in qgr.
`summary_FUN` | function. only relevant if win_method is "summary". passed to `viewGRangesWinSummary_dt`.
`fragLens` | numeric. The fragment length to use to extend reads. The default value "auto" causes an automatic calculation from 100 regions in qgr. NA causes no extension of reads to fragment size.
`target_strand` | character. One of c("*", "+", "-"). Controls filtering of reads by strand. Default of "*" combines both strands.
`anchor` | character, one of c("center", "center_unstranded", "left", "left_unstranded")
`names_variable` | The column name where unique_names are stored.
`return_data.table` | logical. If TRUE the internal data.table is returned instead of GRanges. Default is FALSE.

### Details

if `qgr` contains the range chr1:1-100 and `win_size` is 10, values from positions chr1 5,15,25...85, and 95 will be retrieved from `bw_file`

### Value

A tidy formatted GRanges (or data.table if specified) containing fetched values.

### Examples

    if(Sys.info()['sysname'] != "Windows"){
    library(GenomicRanges)
    bam_f = system.file("extdata/test.bam",
        package = "seqsetvis", mustWork = TRUE)
    bam_files = c("a" = bam_f, "b" = bam_f)
    qgr = CTCF_in_10a_overlaps_gr[1:5]
    bw_gr = ssvFetchBam(bam_files, qgr, win_size = 10)
    bw_gr2 = ssvFetchBam(as.list(bam_files), qgr, win_size = 10)

    bw_dt = ssvFetchBam(bam_files, qgr, win_size = 10,
        return_data.table = TRUE)
    }

[Package seqsetvis version 1.0.2 Index]