diagPoisBG {GeoDiff}R Documentation

Perform diagnosis on Poisson background model

Description

Perform diagnosis on Poisson background model

Perform diagnosis on Poisson background model

Usage

diagPoisBG(object, ...)

## S4 method for signature 'NanoStringGeoMxSet'
diagPoisBG(
  object,
  split = FALSE,
  padj = FALSE,
  padj_method = "BH",
  cutoff = 1e-06,
  generate_ppplot = TRUE
)

## S4 method for signature 'list'
diagPoisBG(
  object,
  padj = FALSE,
  padj_method = "BH",
  cutoff = 1e-06,
  generate_ppplot = TRUE
)

Arguments

object

a list of sizefact, featfact, countmat, or id (if it is for mutliple slides)

...

additional argument list that might be used

split

indicator variable on whether it is for multiple slides (Yes, TRUE; No, FALSE)

padj

whether to adjust p value for outlier detection, default =TRUE

padj_method

p value adjustment method, default ="BH"

cutoff

p value(or adjusted p value) cutoff to determine outliers

generate_ppplot

whether to generate ppplot, default =TRUE

Value

a valid S4 object

a list of following items

Examples

data(demoData)
demoData <- fitPoisBG(demoData, size_scale = "sum")
demoData <- diagPoisBG(demoData)
Biobase::notes(demoData)$disper
demoData <- fitPoisBG(demoData, groupvar = "slide name")
demoData <- diagPoisBG(demoData, split = TRUE)
Biobase::notes(demoData)$disper_sp

[Package GeoDiff version 0.99.5 Index]