Calculates CV This function only calculates inter-plate CV for targets that are present across all plates in the data_list. Any targets that are present on only a subset of plates will be excluded. In addition, individual targets, such as internal controls, can be explicitly excluded using the exclude_targets argument.
interCV(
data_list,
samples,
aboveLOD = NULL,
exclude_targets = NULL,
useMean = TRUE,
method = "count"
)A list of data matrices that contain data for the sample replicates for calculating inter-plate CV.
A list of vectors of length equal to the number of columns in the corresponding data matrix which encodes the sets of sample replicates that will be used to calculate inter-plate CVs. Can be a list of either numeric or character vectors, where matching entries represent replicates for a given sample. Any NAs in the sample vectors will be excluded (it may be desirable to exclude negative controls or inter-plate controls, for example). Unique entries of these vectors will be used to identify unique sample replicate sets in the results output.
A list of logical TRUE/FALSE matrices output by the NULISAseqR::lod() function. Indicates which values to include / exclude in the CV calculation. Default is NULL, which includes all values in CV calculation.
A list of vectors of row names or row indices representing the targets that should be excluded from intra-plate CV calculation. For example, one might want to exclude internal controls. Default is NULL, which includes all common targets in the data_list matrices.
A logical TRUE / FALSE that indicates whether or not to calculate inter-CV using the intra-plate means of replicates (TRUE, default), or to use the pooled replicate data (FALSE).
Use "count" (default) for unnormalized or
normalized count data. Calculates CV using the formula
cv = sd / mean. Use "log2" for log2 transformed data. Calculates CV using
the formula sigma = sd(x) log(2) and
cv = 100 sqrt(exp(sigma^2)-1).
matrix with inter-plate