Validate cells present in fragment file

Search for a fragment from each cell that should exist in the fragment file. Will iterate through chunks of the fragment file until at least one fragment from each cell barcode requested is found.

Usage

ValidateCells(
  object,
  cells = NULL,
  tolerance = 0.5,
  max.lines = 5e+07,
  verbose = TRUE
)

Arguments

object

A Fragment2 object

cells

A character vector containing cell barcodes to search for. If NULL, use the cells stored in the Fragment object.

tolerance

Fraction of input cells that can be unseen before returning TRUE. For example, tolerance = 0.01 will return TRUE when 99% of cells have observed fragments in the file. This can be useful if there are cells present that have much fewer total counts, and would require extensive searching before a fragment from those cells are found.

max.lines

Maximum number of lines to read in without finding the required number of cells before returning FALSE. Setting this value avoids having to search the whole file if it becomes clear that the expected cells are not present. Setting this value to NULL will enable an exhaustive search of the entire file.

verbose

Display messages