fitPoisBG_sp-methods: Estimate Poisson background model for multiple slides

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

Estimate Poisson background model for multiple slides

Description

Estimate Poisson background model for multiple slides:

Usage

fitPoisBG_sp(object, ...)

## S4 method for signature 'matrix'
fitPoisBG_sp(
  object,
  id,
  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
id	character vector same size as sample size representing slide names of each sample
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 list of following items

• sizefact - estimated size factor

• featfact - estimated feature factor matrix, column names the same as the slide id

• countmat - the input count matrix

• id - the input id

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