buildBatch: Batch Builder

Description

Prepares XML node for ExportToBATCH.

Usage

buildBatch(
  files,
  compensation,
  analysis,
  default_batch_dir,
  config_file,
  name = "Batch1",
  use_acquisition = FALSE,
  suffix = "",
  allow_channels_dissimilarity = FALSE,
  overwrite = TRUE,
  segment_rif = "None",
  options
)

Value

a list containing batch information:

-xml, the xml object to be written,

-batch_dir, the directory where xml file is desired to be saved according to 'default_batch_dir' and 'config_file'.

Arguments

files: path of files to batch.
compensation: path to compensation file.
analysis: path to analysis file.
default_batch_dir: directory where batches are stored.
It can be found in IDEAS(R) software, under Options -> Application Defaults -> Directories -> Default Batch Report Files Directory.
If missing, the default, it will be deduced from IDEAS(R) config file, However, if it can't be deduced then tempdir(check = TRUE) from base will be used.
This argument takes precedence over 'config_file' and filling 'default_batch_dir' prevents the use of 'config_file' argument.
config_file: path to IDEAS(R) config file.
It may depends on IDEAS(R) software installation but one may use "C:/Users/%USER%/AppData/Roaming/Amnis Corporation/userconfig.xml".
name: name of batch. Default is "Batch1".
use_acquisition: whether to use acquisition as analysis template. Default is FALSE.
suffix: suffix to add to files when batched. Default is "".
allow_channels_dissimilarity: whether to allow building batch when all files were not acquired with same channels. Default is FALSE.
overwrite: whether to overwrite files or not. Default is TRUE.
segment_rif: size of file segmentation. Default is "None", for no segmentation.
Allowed are "None", "100", "1K", "5K", "10K", "50K", "100K".
options: A list of arguments to be passed.
If missing, the default, options will be set to:
-"Brightfield compensation"=TRUE,
-"EDF deconvolution"=TRUE,
-"Camera background"=TRUE,
-"Spatial alignment"=TRUE.
Allowed are TRUE or FALSE for all, excepted for 'Spatial aligment' which can also be path to .rif file.