ssvFetchBamPE.RNA: ssvFetchBamPE.RNA

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

ssvFetchBamPE.RNA

Description

ssvFetchBamPE.RNA

Usage

ssvFetchBamPE.RNA(
  file_paths,
  qgr,
  unique_names = NULL,
  win_size = 50,
  target_strand = "both",
  absolute_strand = FALSE,
  splice_strategy = "ignore",
  return_data.table = FALSE,
  win_method = "sample",
  max_dupes = Inf,
  flip_strand = FALSE,
  sum_reads = TRUE,
  n_cores = getOption("mc.cores", 1),
  force_skip_centerFix = TRUE,
  n_region_splits = 1
)

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.
target_strand	character. if one of "+" or "-", reads are filtered to match. ignored if any other value.
absolute_strand	If TRUE, strandedness of qgr will be ignored. This is useful when creating tracks for similar.
splice_strategy	character, one of c("none", "ignore", "add", "only", "splice_count"). Default is "none" and spliced alignment are asssumed not present. fragLen must be NA for any other value to be valid. "ignore" will not count spliced regions. add" counts spliced regions along with others, "only" will only count spliced regions and ignore others.
return_data.table	logical. If TRUE the internal data.table is returned instead of GRanges. Default is FALSE.
win_method	character. one of c("sample", "summary"). "sample" selects values at intervals and "summary" applies a weight mean function to all values in window.
max_dupes	numeric >= 1. duplicate reads by strandd start position over this number are removed, Default is Inf.
flip_strand	logical. if TRUE strands are flipped.
sum_reads	logical. If true R1 and R2 reads are added together. If FALSE they are returned separately, identified by the "read" attribute.
n_cores	integer number of cores to use. Uses mc.cores option if not supplied.
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".
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.

Value

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

Examples

library(GenomicRanges)
pkg_dir = system.file(package = "seqsetvis", "extdata", mustWork = TRUE)
bam_files_esr1 = dir(pkg_dir, pattern = "H1.+R1.ESR1_RNA.+bam$", full.names = TRUE)
names(bam_files_esr1) = sub("_R.+", "", basename(bam_files_esr1))
query_gr = GenomicRanges::GRanges("chr6:151656691-152129619:+")
query_gr = GenomicRanges::GRanges("chr6:152116691-152129619:+")

strand(query_gr) = "+"

prof_dt = ssvFetchBamPE.RNA(bam_files_esr1, query_gr, return_data.table = TRUE, win_size = 1)
prof_dt

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.