makeExampleOutriderDataSet: Create example data sets for OUTRIDER

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Create example data sets for OUTRIDER

Description

Creates an example data set from a file or simulates a data set based on random counts following a negative binomial distribution with injected outliers with a fixed z score away from the mean of the gene.

Usage

makeExampleOutriderDataSet(
  n = 200,
  m = 80,
  q = 10,
  freq = 0.001,
  zScore = 6,
  inj = c("both", "low", "high"),
  sf = rnorm(m, mean = 1, sd = 0.1),
  dataset = c("none", "GTExSkinSmall", "KremerNBaderSmall")
)

Arguments

n	Number of simulated genes
m	Number of simulated samples
q	number of simulated latend variables.
freq	Frequency of in-silico outliers
zScore	Absolute z score of in-silico outliers (default 6).
inj	Determines whether counts are injected with the strategy ('both', 'low', 'high'), default is 'both'.
sf	Artificial Size Factors
dataset	If "none", the default, an example data set is simulated. One can also use example data set included in the package by specifying 'GTExSkinSmall' or 'KremerNBaderSmall'

Value

An OutriderDataSet containing an example dataset. Depending on the parameters it is based on a real data set or it is simulated

Examples

# A generic dataset 
ods1 <- makeExampleOutriderDataSet()
ods1

# A generic dataset with specificed sample size and injection method
ods2 <- makeExampleOutriderDataSet(n=200, m=50, inj='low')
ods2

# A subset of a real world dataset from GTEx 
ods3 <- makeExampleOutriderDataSet(dataset="GTExSkinSmall")
ods3

gagneurlab/OUTRIDER documentation built on April 29, 2024, 2:22 a.m.