Read 'Agilent' ACAML files — read_acaml • chromConverter

Extracts injection metadata from 'Agilent Common Analytical Markup Language' (ACAML) files into a table.

Usage

read_acaml(
  path,
  find_files,
  format_out = c("data.frame", "data.table", "tibble"),
  progress_bar = FALSE,
  cl = 1
)

Arguments

path: Path(s) to ACAML files or to folders that contain the files.
find_files: Logical. Whether to treat the supplied paths as directories to search for files. Inferred if not supplied, by testing whether every path is a file.
format_out: Class of output. Either matrix, data.frame, or data.table.
progress_bar: Logical. Whether to show a progress bar. Defaults to FALSE, unlike read_chroms, because an ACAML file usually accompanies a sequence rather than arriving in bulk: read_agilent_rslt calls this function on the single .acaml file in a .rslt directory, where a progress bar over one element is just noise.
cl: Argument to pbapply specifying the number of parallel workers to use or a cluster object created by makeCluster (a set of parallel R worker processes). Defaults to 1.

Value

A data.frame, data.table or tibble (according to the value of format_out) with one row per injection, and a SourceFile column naming the ACAML file it came from.

Details

ACAML is an XML-based format used by Agilent OpenLab to store sequence and sample metadata. This function extracts information from the InjectionMetaData nodes embedded in the InjectionMetaDataItems custom field files, which do not seem to be readily accessible through other means.

Examples

if (FALSE) { # \dontrun{
read_acaml(path)
} # }