make_scc_dt.single: make_scc_dt.single

In jrboyd/seqqc:

Description

based on peakrefine::calcSCCMetrics

Usage

make_scc_dt.single(
  bam_file,
  query_gr,
  frag_sizes,
  fetch_size = 3 * max(frag_sizes),
  cache_path = "~/.cache_peakrefine",
  cache_version = "v1",
  force_overwrite = FALSE,
  n_cores = getOption("mc.cores", 1L),
  ...
)

Arguments

bam_file	a single path to a bam file
query_gr	GRanges of regions to calculate SCC for
frag_sizes	optional numeric. Fragment sizes to calculate correlation at. The higher the resolution the longer calculation will take. The default is to count by 10 from 50 to 350.
fetch_size	optional numeric. Size in bp centered around each interval in query_gr to retrieve. Should be greater than max frag_size. The default is 3*max(frag_sizes).
cache_path	path to cache location for BiocFileCache to use.
cache_version	Modifying the cache version will force recalulation of all results going forward. Default is v1.
force_overwrite	Logical, if TRUE, cache contents will be overwritten.
n_cores	Number of cores to use. Defaults to mc.cores if set or 1.
...	passed to Rsamtools::ScanBamParam()

Value

list fo tidy data.table of SCC data for bam_file

Examples

peak_file = dir(system.file("extdata", package = "seqqc"),
  pattern = "test_peaks.bed$", full.names = TRUE)
bam_file = dir(system.file("extdata", package = "seqqc"),
  pattern = "test_peaks.bam$", full.names = TRUE)

query_gr = seqsetvis::easyLoad_bed(peak_file)[[1]]

scc_res = seqqc:::make_scc_dt.single(bam_file, query_gr, seq(50,300, by = 10))

jrboyd/seqqc documentation built on March 20, 2021, 2:04 p.m.