read_LIMS_SBA_files: Parse a set of constituent files exported from LIMS for a...
In Rundmus/BAf-R_package: Binder Array data hanlding package in facility

Description Usage Arguments Value Author(s) See Also

A set of files for a project can be obtained from "Project Summary" in LIMS. This function reads the set and construct an object of BAf class parsing the files. Because this function is so sensitive to the format of data, the functionality of the current version of this function can limited to present-day form (2014-03-04) only with limited backward compatibility. Please, note that any change in LIMS can affect this function. Optionally, it produces some plots in technical aspects.

read_LIMS_SBA_files(
  SLid,
  path,
  ...,
  QC_plot = FALSE,
  QC_report = FALSE,
  author = "Mun-Gwan",
  path_QC = "../QC",
  lowbound_mfi = 100
)

`SLid`	the sample layout ID used in LIMS, e.g. "SL0001". Currently it is the first six letters in all constituent files.
`path`	the path to the files from LIMS
`...`	for the future
`QC_plot`	whether the plots in technical aspects should be drawn, such as intentisy distribution plots across samples or antibodies.
`QC_report`	whether a primary QC report to be written invoking `write_primary_QC_report.SBA` or not
`author`	the author of the report
`path_QC`	where the QC plots or QC report to be saved
`lowbound_mfi`	the lower bound of MFI. If a median of a sample is below this threshold, the data of the sample is neglected afterwords in QC report.