validate_cells {microdiluteR}

Check validity of each cell in data frame.

Description

validate_cells checks if samples are valid based on either a user-set threshold (i.e. a maximum absorption value) or a list of invalid samples provided by the user.

apply_validation_method evaluates whether a sample meets a user-set validity criteria based on a specified validity method.

ask_validity_method applies a user prompt to check for the validation method to apply on the samples. This can be either 'threshold' (then a maximum absorption value is asked via a call to function ask_threshold) or 'samples'

ask_threshold applies a user prompt to check for a valid absorption maximum used as a threshold.

ask_invalid_samples applies a user prompt to check for invalid samples.

update_validity updates the Validity column in a dataframe based on a specified position and combinations of factors. It sets the Validity to "invalid" for rows where the Position matches the specified position and where the combinations of factors A, B, and C match the provided group levels.

Usage

validate_cells(
  raw_data,
  row_names,
  col_names,
  validity_method = c("threshold", "samples"),
  threshold = NULL,
  invalid_samples = NULL
)

apply_validation_method(
  value,
  i,
  j,
  row_names,
  col_names,
  validity_method = c("threshold", "samples"),
  threshold = NULL,
  invalid_samples = NULL
)

ask_validity_method()

ask_threshold()

ask_invalid_samples()

update_validity(
  input_data,
  wp_var = "Position",
  well_positions,
  group_levels = NULL
)

Arguments

raw_data

The original data frame.

row_names

Names or identifiers of rows in the matrix or data frame.

col_names

Names or identifiers of columns in the matrix or data frame.

validity_method

The method used to determine validity. Either 'threshold' or 'samples'.

threshold

A threshold value used for determining validity. Only applied if 'validity_method is set to 'threshold'.

invalid_samples

A container for storing invalid samples or their indices. Only applied if 'validity_method is set to 'samples'.

value

The value to be checked for validity.

i

The row index of the value in the matrix or data frame.

j

The column index of the value in the matrix or data frame.

input_data

A dataframe containing the data to be updated.

wp_var

A character string specifying the column providing the well positions. Defaults to "Position".

well_positions

The well positions to filter the data on.

group_levels

A list specifying the combinations of factors A, B, and C to match. Each element of the list should be a vector of factor levels.

Value

validate_cells returns a data frame with validity information

apply_validation_method returns logical value indicating whether the value meets the validity criteria.

The user's validity method preference

ask_threshold returns the user-specified threshold

ask_invalid_samples returns a vector of invalid samples

update_validity returns the updated dataframe with Validity modified accordingly.

See Also

generate_experiment_list, ask_experiment_list, generate_group_list, ask_group_list, add_treatment, add_concentration, validate_cells

Examples

df <- data.frame(Position = c("pos1", "pos2", "pos2", "pos4", "pos4"),
                 Value = c(1, 2, 3, 4, 5),
                 Validity = c("valid", "valid", "valid", "valid", "valid"),
                 A = c("a1", "a2", "a3", "a1", "a2"),
                 B = c("b1", "b2", "b3", "b1", "b2"),
                 C = c("c1", "c2", "c3", "c1", "c2"))
updated_df <- update_validity(df,
                              well_positions = "pos2",
                              group_levels = list(A = c("a2", "a3"), B = c("b2", "b3")))
updated_df