CalculateSynergy {synergyfinder} | R Documentation |
CalculateSynergy
is the main function for calculating synergy scores
based on model(ZIP, Bliss, Loewe, and HSA) fron one dose-response
matrix.
CalculateSynergy(data, method = "ZIP", adjusted = TRUE, data.type = "viability")
data |
a list object generated by function |
method |
a parameter to specify which models to use to calculate the synergy scores. Choices are "ZIP", "Bliss", "HSA" and "Loewe". Defaults to "ZIP". |
adjusted |
a logical value. If it is |
data.type |
a parameter to specify the response data type which can be either "viability" or "inhibition". |
The steps for calculation:
Pre-process Matrix
Impute for missing values (with the average of values from the
nearest four cells) in original matrix by using function
ImputeNA
.
Add noise(A small random number ranging from 0 to 0.001) to
original matrix by using function line{AddNoise}
.
)
Correct baseline to 0, if correction
is TRUE
.
Calculate synergy scores using the functions:
a list. It contains 4 elements:
dose.response.mats The original input dose-response matrix
adjusted.response.mats The dose response matrix adjusted
by functions: AddNoise
, ImputeNA
, and
CorrectBaseLine
.
drug.pairs a data frame contains the name of the row drug, the name of the column drug, concentration unit and block IDs.
scores It contains the modified response value and 4 type of synergy scores of each drug dose response pair.
method the method used to calculate the synergy scores.
Liye He liye.he@helsinki.fi
Shuyu Zheng shuyu.zheng@helsinki.fi
data("mathews_screening_data") data <- ReshapeData(mathews_screening_data) scores <- CalculateSynergy(data)