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Read 'Agilent' ACAML files from directory.

Source: R/read_acaml.R
read_acaml.Rd

Extracts injection metadata from 'Agilent Common Analytical Markup Language' (ACAML) files into an R object.

Usage

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

Arguments

path

Path(s) to ACAML files or to folders that contain the files.

find_files

Logical. Set to TRUE (default) if you are providing the function with a folder or vector of folders containing the files. Otherwise, set to FALSE.

format_out

Class of output. Either matrix, data.frame, or data.table.

progress_bar

Logical. Whether to show progress bar. Defaults to TRUE if pbapply is installed.

cl

Argument to pbapply specifying the number of clusters to use or a cluster object created by makeCluster. Defaults to 1.

Value

A data.frame, data.table or tibble (according to the value of format_out) containing sample metadata derived from the supplied ACAML files.

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.