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Write Agilent AMX method file

Source: R/write_agilent_amx.R
write_agilent_amx.Rd

Writes a copy of an 'OpenLab CDS' acquisition method (.amx) with a new pump gradient, flow, stop time, post time or column temperature. All other settings are copied unchanged from the template.

Usage

write_agilent_amx(
  path,
  path_out,
  gradient = NULL,
  flow = NULL,
  stop_time = NULL,
  post_time = NULL,
  temperature = NULL,
  force = FALSE
)

Arguments

path

Path to the template .amx file.

path_out

Path to write the new method.

gradient

A table of solvent composition over time (see Details). NULL (default) keeps the template's gradient.

flow

Flow rate in mL/min. NULL (default) keeps the template's value.

stop_time

Pump stop time in minutes. NULL (default) keeps the template's value.

post_time

Pump post time in minutes, at least 0.01. 0 turns the post time off. NULL (default) keeps the template's value.

temperature

Column temperature in degrees Celsius. NULL (default) keeps the template's value.

force

Whether to overwrite path_out if it exists. Defaults to FALSE.

Value

Invisibly returns path_out.

Details

The writer has only been tested on methods for a G7104C quaternary pump and a G7116A column compartment. Other modules may lay out their methods differently. If the writer fails on one of your methods, or writes one that OpenLab will not load, please open an issue and attach the template. Open each written method in OpenLab and check its settings before you run it.

gradient takes the table that read_agilent_amx() returns as pump$gradient, in wide or long format. It needs a percentage for every solvent channel the template uses, and each row must add up to 100. It must have a row at time zero, which sets the starting composition. The other rows replace the composition steps in the pump timetable. Flow steps in the timetable are kept, and gradient cannot change them. If the template has flow steps, drop the flow_mL_min column (or the "flow" rows in long format) from the table read_agilent_amx() returns.

Setting flow gives a constant flow rate and removes the template's flow steps.

temperature sets both sides of the column compartment, and the template must already control the temperature. A template whose compartment is set to "Not Controlled" gives an error.

Setting stop_time also sets the run time of the method. The checksum of each edited part is recalculated. The Agilent/ReportableInformation part, which repeats the settings as formatted text, is not rewritten and still describes the template.

The writer needs the 'zip' package.

See also

read_agilent_amx()

Other write functions: write_andi_chrom(), write_andi_ms(), write_chroms(), write_mzml()

Examples

if (FALSE) { # \dontrun{
gradient <- data.frame(time_min = c(0, 2, 8),
                       pct_A = c(70, 70, 5),
                       pct_B = c(30, 30, 95))
write_agilent_amx("template.amx", "new.amx", gradient = gradient,
                  stop_time = 10)
} # }