ssvFetchBam.scRNA: Title

In jrboyd/ssvRecipes: Recipes using seqsetvis

Title

Description

Title

Usage

ssvFetchBam.scRNA(
  file_path,
  qgr,
  cell_cluster_assignments,
  cell_cluster_id_ = "seurat_clusters",
  id_prefixes = "",
  unique_names = NULL,
  win_size = 50,
  win_method = c("sample", "summary")[1],
  summary_FUN = stats::weighted.mean,
  target_strand = c("*", "+", "-", "both")[1],
  flip_strand = FALSE,
  anchor = c("left", "left_unstranded", "center", "center_unstranded")[3],
  names_variable = "sample",
  return_data.table = FALSE,
  max_dupes = Inf,
  splice_strategy = c("none", "ignore", "add", "only", "splice_count")[2],
  n_cores = getOption("mc.cores", 1),
  return_unprocessed = FALSE,
  force_skip_centerFix = FALSE,
  force_barcodes = FALSE,
  min_seq_qual = 0,
  ...
)

Arguments

file_path	character vector of file_path to load from. Alternatively, file_path 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.
cell_cluster_assignments	either a list of character vectors containing cell ids or a data.table. If data.table one column bust be 'id' and contain cell barcodes, the other must match cell_cluster_id_ and contain cluster names.
cell_cluster_id_	Attribute name of cell_cluster_assignments where cell barcodes are stored.
id_prefixes	Character prefix to prepend to cell barcodes retrieved from bam files such that they match id items in cell_cluster_assignments. Either a single item to reuse or character vector of length equal to number of bam files. Default of "" adds nothing.
unique_names	not used. see cell_cluster_assignments for analogous functionality.
...

jrboyd/ssvRecipes documentation built on May 22, 2022, 7:07 a.m.