map a single plate_map to a read promega_plate

Where there are repeated experiment columns, give them a suffix to indicate the number of technical replicates, and more importantly prevent automatic suffix addition in R to prevent unexpected results. This acts as a daughter function of plate_map_onto_plate but also can act as a stand alone function.

validate the columns of neg, pos, or samples

now treat each unique virus suffix as their own set, and normalise.

Usage

adding_technical_replicate_suffix(mapped_plate)

plateMap_map_onto_promega_read(plate_map, promega_read_values)

validate_columns(columns)

convert_dilution_factor(dilution_factor_string = "1 in 3")

generate_dilution_series(
  Starting_Dilution_or_concentration = 20,
  num_steps = 8,
  dilution_factor = "1 in 3",
  titration_mode = c("dilution", "concentration")
)

normalise_plate_using_plateMap(
  plate_map = plate1_map,
  processed_read_values_with_tech_rep
)

Arguments

mapped_plate

the dataframe of values which columns are assigned but may have repeated columns

plate_map

platemap with the strict platemap format

promega_read_values

promega_plate_df generated from read_promega_plate_xlsx.R , if not specified, the plate_map column promega_plate_path will be searched

columns

Negative_Control_Column, Positive_Control_Column, or column from a plate map, which can be strings like "5,6" when processing experiment columns which summarises

dilution_factor_string

dilution formatted as numerator in denominator (e.g. 1 in 3)

Starting_Dilution_or_concentration

The starting dilution or concentration (unitless)

num_steps

Number of dilution rows including neat

dilution_factor

dilution formatted as numerator in denominator (e.g. 1 in 3)

titration_mode

If dilution, the numbers get bigger, if concentration, the numbers get smaller

processed_read_values_with_tech_rep

output of plateMap_map_onto_promega_read

Value

a dataframe where all values have _techrepn suffixed, prevents having repeated column names.

normalized values with , <dilution_or_concentration>, <dilution_serie> from plate_map

validated version which is a list of integers

numeric dilution_factor

comma-separated string of dilution_series

validated version which is a list of integers