Calculates limit of detection (LoD) for each target based on the negative controls (blanks). LoD = mean(blanks) + 3*SD(blanks). Designates data as either above or below LoD. Option to specify minimum count threshold for detectability.
lod(
data_matrix,
blanks,
min_count = 0,
min_blank_no = 4,
mad_threshold = 2.5,
ignore_target_blank = NULL,
targetNoOutlierDetection = NULL,
match_matrix = NULL
)The Data matrix output from readNULISAseq.R or normalized data from normalization functions.
Column indices or column names of the blanks in the data_matrix.
Optional count threshold to apply in addition to the LoD. Default is 0.
Optional numeric parameter defining the minimum number of blanks required to enable MAD outlier detection and removal. Default is 4.
Optional numeric parameter defining the threshold used for MAD outlier identification. Default is 2.5.
List of targets and corresponding blanks/NCs to exclude. Names of the list represent targets and values which are arrays represent blank/NC names to ignore during LoD calculation.
Option to provide targets which should NOT have outlier detection applied Defaults to NULL.
Matrix of indices provided by calcSampleTargetNAs. Lists samples/targets that should not be reported
Vector of limits of detection.
Logical matrix indicating whether counts are above or below LoD for that target.
A list.