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]