BGScoreTest_sp-methods: Testing for features above the background, multiple slides...

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

Testing for features above the background, multiple slides case

Description

Testing for features above the background using Poisson background model as reference, multiple slides case

Usage

BGScoreTest_sp(object, ...)

## S4 method for signature 'matrix'
BGScoreTest_sp(
  object,
  BGmod,
  adj = 1,
  probenum,
  removeoutlier = FALSE,
  useprior = FALSE
)

Arguments

object	count matrix with features in rows and samples in columns
...	additional argument list that might be used
BGmod	fitted background model, multiple slides case
adj	adjustment factor for the number of probes in each feature, default =1 i.e. each target only consists of one probe
probenum	a vector of numbers of probes in each gene
removeoutlier	whether to remove outlier
useprior	whether to use the prior that the expression level of background follows the Beta distribution, leading to a more conservative test

Value

a list of following items

• pvalues - Background score test pvalues matrix, columns the same as slide names

• scores_sp - Background score test statistics matrix, columns the same as slide names

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