ABSDataSet {ABSSeq} | R Documentation

## ABSDataSet object and constructors

### Description

ABSDataSet object and constructors

### Usage

    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

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

[Package ABSSeq version 1.44.0 Index]