diagPoisBG-methods: Perform diagnosis on Poisson background model

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

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

• lowtail - A matrix of lower tail probabilty, in assay slot

• uptail - A matrix of upper tail probability, in assay slot

• disper (or disper_sp if non single-valued groupvar is provided) - dispersion parameter in experimenetData

• low_outlier - A matrix to indicate lower outliers (0:False, 1:True) in assay slot

• upper_outlier - A matrix to indicate upper outliers (0:False, 1:True) in assay slot

a list of following items

• lowtail - A matrix of lower tail probabilty

• uptail - A matrix of upper tail probability

• disper - dispersion parameter

• outlier - A list of coodinates of lower and upper outliers

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

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