QuanRange | R Documentation |
Compute Quantile Range, a metric representing signal strength for QC purpose
Compute Quantile Range, a metric representing signal strength for QC purpose
QuanRange(object, ...) ## S4 method for signature 'NanoStringGeoMxSet' QuanRange(object, split = FALSE, probs, removeoutlier = FALSE, ...) ## S4 method for signature 'matrix' QuanRange(object, probenum, BGmod, probs, removeoutlier = FALSE)
object |
count matrix with features in rows and samples in columns |
... |
additional argument list that might be used |
split |
indicator variable on whether it is for multiple slides |
probs |
numeric vector of probabilities with values in [0,1] passed to quantile |
removeoutlier |
indicator on whether to remove outliers, default: FALSE |
probenum |
a vector of numbers of probes in each gene |
BGmod |
a list of sizefact, sizefact, countmat, and id (if it is for multiple slides) |
a valid S4 object with probabilities in phenoData
a matrix of quantile range in rows and probs in columns
data(demoData) demoData <- fitPoisBG(demoData, size_scale = "sum") demoData <- diagPoisBG(demoData) demoData <- aggreprobe(demoData, use = "cor") Biobase::notes(demoData)$disper demoData <- QuanRange(demoData, split = FALSE, probs = c(0.75, 0.8, 0.9, 0.95)) data(demoData) demoData <- fitPoisBG(demoData, groupvar = "slide name") demoData <- diagPoisBG(demoData, split = TRUE) demoData <- aggreprobe(demoData, use = "cor") Biobase::notes(demoData)$disper_sp demoData <- QuanRange(demoData, split = TRUE, probs = c(0.75, 0.8, 0.9, 0.95))
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