fitPoisBG-methods: Estimate Poisson background model for either single slide or...

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

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

• sizefact - estimated size factor in phenoData

• featfact - estimated feature factor in featureData

a valid GeoMx S4 object if split is TRUE,

• sizefact - estimated size factor in phenoData

• featfact_XX - estimated feature factor vector, column name (denoted as XX) the same as the slide id, in featureData for each unique slide

• fitPoisBG_sp_var - the column name for slide, in experimentData

a list of following items

• sizefact - estimated size factor

• featfact - estimated feature factor

• countmat - the input count matrix

Examples

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

Nanostring-Biostats/GeoDiff documentation built on April 11, 2024, 5:31 a.m.