ssvFetchBamPE {seqsetvis} | R Documentation

## ssvFetchBam for paired-end ChIP-seq files. Only concordant reads are considered, but this has been minimally tested, please verify.

### Description

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

### Usage

    ssvFetchBamPE(
      file_paths,
      qgr,
      unique_names = NULL,
      win_size = 50,
      win_method = c("sample", "summary")[1],
      summary_FUN = stats::weighted.mean,
      anchor = c("left", "left_unstranded", "center", "center_unstranded")[3],
      names_variable = "sample",
      return_data.table = FALSE,
      max_dupes = Inf,
      n_cores = getOption("mc.cores", 1),
      n_region_splits = 1,
      min_isize = 1,
      max_isize = Inf,
      return_unprocessed = FALSE,
      return_fragSizes = FALSE,
      force_skip_centerFix = FALSE,
      ...
    )

### Arguments

`file_paths` | character vector of file_paths to load from. Alternatively, file_paths can be a data.frame or data.table whose first column is a character vector of paths and additial columns will be used as metadata.
`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`.
`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.
`max_dupes` | numeric >= 1. duplicate reads by strandd start position over this number are removed, Default is Inf.
`n_cores` | integer number of cores to use.
`n_region_splits` | integer number of splits to apply to qgr. The query GRanges will be split into this many roughly equal parts for increased parallelization. Default is 1, no split.
`min_isize` | integer. Read pairs must have an isize greater than or equal to this value. Default is 1.
`max_isize` | integer. Read pairs must have an isize less than or equal to this value. Default is Inf.
`return_unprocessed` | boolean. if TRUE returns read alignment in data.table. Default is FALSE.
`return_fragSizes` | boolean. if TRUE returns fragment sizes for all reads per region.
`force_skip_centerFix` | boolean, if TRUE all query ranges will be used "as is". This is already the case by default if win_method == "summary" but may have applications where win_method == "sample".
`...` | passed to Rsamtools::ScanBamParam() Uses mc.cores option if not supplied.

### Details

#' In contrast to ssvFetchBam, extension of reads to estimated fragment size is not an issue as each read pair represents a fragment of exact size.

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

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/Bcell_PE.mm10.bam",
        package = "seqsetvis", mustWork = TRUE)
    bam_files = c("a" = bam_f, "b" = bam_f)
    data("Bcell_peaks")
    qgr = Bcell_peaks
    bw_gr = ssvFetchBamPE(bam_files, qgr, win_size = 10)
    bw_gr2 = ssvFetchBamPE(as.list(bam_files), qgr, win_size = 10)

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

[Package seqsetvis version 1.14.4 Index]