fitPoisthNorm_sp {GeoDiff}R Documentation

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


[Package GeoDiff version 1.0.0 Index]