stsFetchTsneInput: stsFetchTsneInput

In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

stsFetchTsneInput

Description

retrieve data from series of either bigwig or bam files to a tidy data.table for later input to stsRunTsne

Usage

stsFetchTsneInput(
  qdt,
  qgr,
  region_size = NULL,
  file_format = NULL,
  qwin = 50,
  qmet = "summary",
  cap_value = 20,
  fetch_FUN = NULL,
  agg_FUN = NULL,
  high_on_right = TRUE,
  bfc = BiocFileCache::BiocFileCache(),
  n_cores = getOption("mc.cores", 1),
  rname = digest::digest(list(qgr, qdt, qwin, qmet, fetch_FUN)),
  force_overwrite = FALSE,
  verbose = TRUE,
  skip_checks = FALSE
)

Arguments

qdt	data.table containing, file, tall_var, wide_var, and optionally norm_factor
qgr	GRanges of regions to fetch
region_size	numeric, if provided will be used to set all widths on qgr.
file_format	character, describing file format. must be one of bam or bw. Will be automatically determined from file extension if NULL.
qwin	number of datapoints to use to view each region
qmet	strategy to use in each region, summary or sample
cap_value	maximum allowed value. useful for outlier handling.
fetch_FUN	function used to load and process data from files.
agg_FUN	function used to aggregate any duplicate tall_var+wide_var mappings in qdt. Should accept a numeric vector and return a single value.
high_on_right	if TRUE, profiles where highest signal is on the left are flipped.
bfc	BiocFileCache object to use to cache data
n_cores	number of cores to use. Defaults to value of mc.cores or 1 if mc.cores is not set.
rname	rname to use with cache. Default is a digest of arguments used to fetch data.
force_overwrite	if TRUE, any contents of cache are overwritten. Default is FALSE.
verbose	if TRUE outputs progress and log messages
skip_checks	if TRUE, tall_var and wide_var completeness checks are skipped. tall_var/wide_var combinations must be complete to run StsRunTsne(). Default is FALSE.

Details

validates inputs prepares query_gr fetches either bam or bigwig based on extension of first file transform and normalizes profiles after fetch

Value

a tidy data.table of profile data.

Examples

data("query_gr")
bw_files = dir(system.file('extdata', package = "chiptsne"), pattern = ".bw$", full.names = TRUE)
cfg_dt = data.table(file = bw_files)
cfg_dt[, c("tall_var", "wide_var") := tstrsplit(basename(file), "_", keep = 1:2)]
cfg_dt = cfg_dt[tall_var %in% c("ESH1", "HUES48", "HUES64")]
cfg_dt[, norm_factor := ifelse(wide_var == "H3K4me3", .3, 1)]
profile_dt = stsFetchTsneInput(cfg_dt, query_gr)
profile_dt

jrboyd/seqtsne documentation built on Nov. 5, 2022, 6:37 a.m.