ssvFetchBigwig: Iterates a character vector (ideally named) and calls...

Description Usage Arguments Details Value Examples

View source: R/functions_fetch_bigwig.R

Description

ssvFetchBigwig iteratively calls fetchWindowedBigwig.single. See ssvFetchBigwig.single for more info.

Usage

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ssvFetchBigwig(file_paths, qgr, unique_names = names(file_paths),
  names_variable = "sample", win_size = 50, win_method = c("sample",
  "summary")[1], summary_FUN = stats::weighted.mean, anchor = c("left",
  "left_unstranded", "center", "center_unstranded")[3],
  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.

names_variable

The column name where unique_names are stored. 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")

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

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if(Sys.info()['sysname'] != "Windows"){
library(GenomicRanges)
bw_f = system.file("extdata/test_loading.bw",
    package = "seqsetvis", mustWork = TRUE)
bw_files = c("a" = bw_f, "b" = bw_f)
qgr = GRanges("chrTest", IRanges(1, 30))
bw_gr = ssvFetchBigwig(bw_files, qgr, win_size = 10)
bw_gr2 = ssvFetchBigwig(as.list(bw_files), qgr, win_size = 10)

bw_dt = ssvFetchBigwig(bw_files, qgr, win_size = 10,
    return_data.table = TRUE)
}

jrboyd/seqsetvis documentation built on Oct. 28, 2018, 3:16 a.m.