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.
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
#> Position Value Validity A B C
#> 1 pos1 1 valid a1 b1 c1
#> 2 pos2 2 invalid a2 b2 c2
#> 3 pos2 3 invalid a3 b3 c3
#> 4 pos4 4 valid a1 b1 c1
#> 5 pos4 5 valid a2 b2 c2