fitPoisthNorm_sp-methods: Poisson threshold model based normalization-log2...

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

Poisson threshold model based normalization-log2 transformation for multiple slides

Description

Poisson threshold model based normalization-log2 transformation for multiple slides

Usage

fitPoisthNorm_sp(object, ...)

## S4 method for signature 'matrix'
fitPoisthNorm_sp(
  object,
  probenum,
  features_high,
  features_all = colnames(object),
  sizefact_start,
  sizefact_BG,
  threshold_mean,
  preci2 = 10000,
  id,
  iterations = 2,
  prior_type = c("contrast", "equal"),
  sizefactrec = TRUE,
  size_scale = c("sum", "first"),
  sizescalebythreshold = FALSE,
  covrob = FALSE,
  preci1con = 1/25,
  cutoff = 15,
  confac = 1
)

Arguments

object	count matrix with features in rows and samples in columns
...	additional argument list that might be used
probenum	a vector of numbers of probes in each gene
features_high	subset of features which are well above the background
features_all	full feature vector to apply the normalization on
sizefact_start	initial value for size factors
sizefact_BG	size factor for background
threshold_mean	average threshold level
preci2	precision for threshold, default=10000
id	character vector of slide name of each sample
iterations	iteration number, default=2, the first iteration using the features_high to construct the prior for parameters then refit the model on all features. precision matrix for threshold: preci2
prior_type	prior type for preci1, "equal" or "contrast", default="contrast"
sizefactrec	XXXX, default = TRUE
size_scale	method to scale the sizefact, sum(sizefact)=1 when size_scale="sum", sizefact[1]=1 when size_scale="first"
sizescalebythreshold	XXXX, default = FALSE
covrob	whether to use robust covariance in calculating the prior precision matrix 1, default = FALSE
preci1con	The user input constant term in specifying precision matrix 1, default=1/25
cutoff	term in calculating precision matrix 1, default=15
confac	The user input factor for contrast in precision matrix 1, default=1

Value

a list of following items

• threshold0, matrix of estimated threshold for iter=1, features in columns and threshold for different slides in rows.

• threshold, matrix of estimated threshold for iter=2, features in columns and threshold for different slides in rows.

• normmat0, matrix of log2 expression for iter=1, features in columns and log2 expression in rows.

• normmat, matrix of log2 expression for iter=2, features in columns and log2 expression in rows.

• sizefact, estimated sizefact

• sizefact0, estimated sizefact in iter=1

• preci1, precision matrix 1

• Im0, Information matrix in iter=1

• Im, Information matrix in iter=2

• conv0, vector of convergence for iter=1, 0 converged, 1 not converged

• conv, vector of convergence for iter=2, 0 converged, 1 not converged

• features_high, same as the input features_high

• features_all, same as the input features_all

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