fitPoisBG {GeoDiff}R Documentation

Estimate Poisson background model for either single slide or multiple slides

Description

Estimate Poisson background model for either single slide or multiple slides

Estimate Poisson background model:

Usage

fitPoisBG(object, ...)

## S4 method for signature 'NanoStringGeoMxSet'
fitPoisBG(
  object,
  groupvar = NULL,
  iterations = 10,
  tol = 0.001,
  size_scale = c("sum", "first"),
  ...
)

## S4 method for signature 'matrix'
fitPoisBG(object, iterations = 10, tol = 0.001, size_scale = c("sum", "first"))

Arguments

object

count matrix with features in rows and samples in columns

...

additional argument list that might be used

groupvar

the group variable name for slide

iterations

maximum iterations to be run, default=10

tol

tolerance to determine convergence, default = 1e-3

size_scale

method to scale the sizefact, sum(sizefact)=1 when size_scale="sum", sizefact[1]=1 when size_scale="first"

Value

a valid GeoMx S4 object if split is FALSE

a valid GeoMx S4 object if split is TRUE,

a list of following items

Examples


data(demoData)
demoData <- fitPoisBG(demoData, size_scale = "sum")
data(demoData)
demoData <- fitPoisBG(demoData, groupvar = "slide name", size_scale = "sum")

[Package GeoDiff version 0.99.5 Index]