ReshapeData: Pre-process the Response Data for Further Calculation and...

In shuyuzheng/synergyfinder: Calculate and Visualize Synergy Scores for Drug Combinations

Pre-process the Response Data for Further Calculation and Plot

Description

A function to transform the response data from data frame format to dose-response matrices. Several processes could be chose to add noise, impute missing values or correct base line to the dose-response matrix.

Usage

ReshapeData(
  data,
  impute = TRUE,
  impute_method = NULL,
  noise = FALSE,
  seed = NULL,
  iteration = 10,
  data_type = "viability"
)

Arguments

data	drug combination response data in a data frame format
impute	a logical value. If it is TRUE, the NA values will be imputed by mice. Default is TRUE.
impute_method	a single string. It sets the method parameter in function mice to specify the imputation method. Please check the documentation of mice to find the available methods.
noise	a logical value. It indicates whether or not adding noise to to the "response" values in the matrix. Default is TRUE.
seed	a single value, interpreted as an integer, or NULL. It is the random seed for calculating the noise and missing value imputation. Default setting is NULL
iteration	An integer. It indicates the number of iterations for bootstrapping while calculating statistics for data with replicates.
data_type	a parameter to specify the response data type which can be either "viability" or "inhibition".

Details

The input data must contain the following columns: (block_id/BlockId/PairIndex), (drug_row/DrugRow/Drug1), (drug_col/DrugCol/Drug2), (response/Response/inhibition/Inhibition), (conc_r/ConcRow/Conc1), (conc_c/ConcCol/Conc2), and (ConcUnit/conc_r_unit, conc_c_unit/ConcUnit1, ConcUnit2, ConcUnit3)

Value

a list of the following components:

• drug_pairs A data frame contains the name of all the tested drugs, concentration unit, block IDs and a logical column "replicate" to indicate whether there are replicates in the corresponding block.

• response A data frame contains the columns: "concX" concentrations for drugs from input data; "response_origin" response values from input data; "response" % inhibition value for downstream analysis.

• response_statistics A data frame. It will be output if there is block have replicated response values. It contains the block ID, the concentrations for all the tested drugs, and statistics for % inhibition values across replicates (including mean, standard deviation, standard error of mean and 95% confidence interval).

Author(s)

• Shuyu Zheng [e-mail]

• Jing Tang [e-mail]

Examples

data("mathews_screening_data")
# set a random number seed for generating the noises
data <- ReshapeData(mathews_screening_data, seed = 1)

shuyuzheng/synergyfinder documentation built on Feb. 20, 2023, 11:33 p.m.