callDE
takes two vectors representing each gene's significance. They are usually p-values from the target data and synthetic null data.
Usage
callDE(
targetScores,
nullScores,
nlogTrans = TRUE,
FDR = 0.05,
correct = FALSE,
threshold = "BC",
ordering = TRUE
)
Arguments
- targetScores
A named numeric vector of the DE scores from the target data, e.g., the p-values between two clusters from the real data.
- nullScores
A named numeric vector of the DE scores from the synthetic null data, e.g., the p-values between two clusters from the null data.
- nlogTrans
A logical value. If the input scores are p-values, take the
-log10
transformation since Clipper require larger scores represent more significant DE. Default is TRUE.- FDR
A numeric value of the target False Discovery Rate (FDR). Default is 0.05.
- correct
A logical value. If TRUE, perform the correction to make the distribution of contrast scores approximately symmetric. Default is FALSE.
- threshold
A string value of the threshold method. Must be 'BC' or 'DS'.
- ordering
A logic value. If TRUE, order the genes in the returned table by their significance. Default is TRUE.