Estimates per-gene x unit thresholds for positive expression and truncates values below this threshold Uncertain values (in terms of posterior probability of membership) can be set to NA or rounded left or right Thresholds are estimated using a Gaussian mixture model with prior supplied by population estimates.
# S4 method for NanoStringAssay
thresholdNanoString(nsa, include.primers,
exclude.primers, posteriorprob, clip = c("left", "right", "NA"),
debug = FALSE, location.strength = 1, pseudo.counts = 5,
hard.threshold = 3, startLayer = "lCount")NanostringAssay object
primeris to use for population estimates. If missing, then all primers are used.
primers to exclude from population estimates
currently ignored
currently ignored
should extra fields helpful for examining the thresholding be returned as a list?
scaling of prior on location
total strength of prior vs data
location estimates less than this value will be treated as belonging to the "noise cluster"
which layer should be used to threshold. Default 'lCount'.
object of class ThresholdedNanoString if debug=TRUE, otherwise returns nsa with the thresholded expression in layer et
ThresholdedNanoString-class