QuanRange-methods: Compute Quantile Range

In Nanostring-Biostats/GeoDiff: Count model based differential expression and normalization on GeoMx RNA data

Compute Quantile Range

Description

Compute Quantile Range, a metric representing signal strength for QC purpose

Compute Quantile Range, a metric representing signal strength for QC purpose

Usage

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)

Arguments

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)

Value

a valid S4 object with probabilities in phenoData

a matrix of quantile range in rows and probs in columns

Examples

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))

Nanostring-Biostats/GeoDiff documentation built on Dec. 19, 2024, 7:22 p.m.