read_FlexMAP3D_csv: Generate BAf object parsing raw file from FLEXMAP3D
In Rundmus/BAf-R_package: Binder Array data hanlding package in facility

Description Usage Arguments Value Author(s) See Also

This generates an BAf object parsing raw file attained directly from the FLEXMAP3D instrument. The samples with median bead counts lower than 35 are marked as "failed" in @assay$fail_flag

read_FlexMAP3D_csv(
  file,
  assayid,
  sinfo,
  bead,
  sample_batch_c = "plate",
  sbaid,
  bead_count_as_failed = 20,
  bead_count_alert = 35,
  reading_order = 1:nrow(sinfo),
  QC_plot = FALSE,
  path_QC = "../output/QC",
  i_neg_ctrl_sample,
  row_var,
  col_var
)

`file`	name of a file from FLEXMAP3D
`assayid`	the assay ID of this sample set and antibody set.
`sinfo`	a `tbl_df` or `data.frame` that contains information about samples, in which each row is for each sample
`bead`	a `tbl_df` or `data.frame` having bead information. Often it can be obtained from other BAf object. If this is missing, a simple `tbl_df` that has only 'assay' column will be used as default.
`sample_batch_c`	the name of sample batch column in the `sinfo`. e.g. `plate`
`sbaid`	optionally, SBA ID of this antibody set can be given here.
`bead_count_as_failed, bead_count_alert`	the cutoff values for bead count. Labeled in `'fail_flag'` as `'failed'` if the bead count is lower than `bead_count_as_failed`. If it is below `bead_count_alert`, then marked as `'lowBeadCount'`. Not in both cases, it is marked as `'ok'`.
`reading_order`	the integers in which order the sample has read by FlexMAP3D. This parameter allows to accept the experimental data which is conducted in reverse or random order.
`QC_plot`	if TRUE, some plots for quality check-up are generated like that of `read_LIMS_SBA_files`
`path_QC`	where the QC plots will be saved. This is valid only if `QC_plot` is TRUE.
`i_neg_ctrl_sample`	the index of negative control samples such as `EMPTY`. A logical vector of same length as samples can be given.
`row_var, col_var`	When these are given, the variable in `sinfo` is compared with the values of row or column in `file` to confirm the order of samples in `sinfo`.