ABSDataSet {ABSSeq} | R Documentation |
ABSDataSet object and constructors
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)
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 |
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. |
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.
An ABSDataSet object.
counts <- matrix(1:4,ncol=2) groups <- factor(c("a","b")) obj <- ABSDataSet(counts, groups) obj <- ABSDataSet(counts, groups, paired=TRUE)