ABSDataSet: ABSDataSet object and constructors

Description Usage Arguments Details Value Examples

View source: R/AllClasses.R

Description

ABSDataSet object and constructors

Usage

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ABSDataSet(counts, groups, normMethod = c("user", "qtotal", "total", "quartile",
  "geometric", "TMM"), sizeFactor = 0, paired = FALSE, minDispersion = NULL, minRates = 0.1,
  maxRates = 0.3, LevelstoNormFC = 100)

Arguments

counts

a matrix or table with at least two columns and one row,

groups

a factor with two groups, whose length should be equal with sample size

normMethod

method for estimating the size factors, should be one of 'user', 'qtotal', 'total', 'quartile', 'geometric' and 'TMM'. See normalFactors for description.

sizeFactor

size factors for 'user' method, self-defined size factors by user.

paired

switch for differential expression detection in paired samples.

minDispersion

a positive double for user-defined penalty of dispersion estimation

minRates

low bounder rate of baseline estimation for counts difference, default is 0.1

maxRates

up bounder rate of baseline estimation for counts difference, default is 0.3. Setting minRates equal with maxRates will result in a testing on user-define rate,

LevelstoNormFC

maximal level of average standard deviation in fold-change normalization according to expression level, default is 100.

Details

The function contructs an ABSDataSet object with counts table and groups. It also checks the structure of counts and groups.The ABSDataSet is a class, used to store the input values, intermediate calculations and results of an analysis of differential expression. It also contains information for the running time of an analysis.

Value

An ABSDataSet object.

Examples

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counts <- matrix(1:4,ncol=2)
groups <- factor(c("a","b"))
obj <- ABSDataSet(counts, groups)
obj <- ABSDataSet(counts, groups, paired=TRUE)

ABSSeq documentation built on Aug. 12, 2017, 2 a.m.