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Get Sample Details

process_well_sample_details.Rd

process_well_sample_details reads in the plate run layout so sample identifiers can be mapped to the output of the Synergy H1 reader.

Usage

process_well_sample_details(
  filepath,
  sample_type = c("mucus", "fin clip"),
  layout_type = c("split_plate_early_late", "split_plate_late_early",
    "split_plate_spring_winter", "split_plate_winter_spring", "triplicate",
    "single_assay_ots28_early", "single_assay_ots28_late", "single_assay_ots16_spring",
    "single_assay_ots16_winter", "custom"),
  plate_run_id,
  assay_order = NULL,
  custom_layout = NULL
)

Arguments

filepath

Synergy H1 reader output excel file with corresponding plate run layout in a sheet titled "Plate Map"

sample_type

either mucus or fin_clip

layout_type

either split_plate_early_late, split_plate_late_early, split_plate_spring_winter, split_plate_winter_spring, triplicate, single_assay_ots28_early, single_assay_ots28_late, single_assay_ots16_spring, single_assay_ots16_winter

plate_run_id

plate run identifier generated by running add_plate_run()

Value

a table to be passed to process_sherlock():

plate_layout

  • location

  • sample_id

  • sample_type_id

  • assay_id

  • plate_run_id

Details

this function is called when the user wants to interact with the database. There is an alternative version of this function, process_well_sample_details_offline, that processes sherlock output without interacting with the database. The output of this function will be used as the sample_details argument in process_sherlock() i.e. it will be used to connect the generic sample identifiers produced by the Synergy H1 reader to sample identifiers in the database. If the layout_type argument is split_plate, it divide the plate into columns 1:12 and 13:24 and assigns assays based on the following logic:

  • split_plate_early_late: columns 1:12 are OTS 28 Early and columns 13:24 are OTS 28 Late

  • split_plate_late_early: columns 1:12 are OTS 28 Late and columns 13:24 are OTS 28 Early

  • split_plate_spring_winter: columns 1:12 are OTS 16 Spring and columns 13:24 are OTS 16 Winter

  • split_plate_winter_spring: columns 1:12 are OTS 16 Winter and columns 13:24 are OTS 16 Spring

If the layout_type argument is triplicate, the assay ids are assigned as follows:

  • rows A, E, I, and M are OTS 28 Early

  • rows B, F, J, and N are OTS 28 Late

  • rows C, G, K, and O are OTS 16 Spring

  • rows D, H, L, and P are OTS 16 Winter

If the layout_type is one of single_assay_ots28_early, single_assay_ots28_late, single_assay_ots16_spring, or single_assay_ots16_winter, all samples processed in that plate run will be assigned that assay.