ABSSeq (version 1.2.0)

results: Accessor functions for the result from a ABSDataSet

Description

Accessor functions for the result from a ABSDataSet by given names

Usage

"results"(object,cnames)

Arguments

object

an ABSDataSet

cnames

a vecotr of names for output, which are among:

'baseMean': average expression for each gene including all samples,

'Amean' and 'Bmean': average expression for each group:A and B,

'absD': absolute expression differences between two groups,

'foldChange': log2 of fold-change for each gene based on B vs. A,

'Variance': variance for each gene

'pvalue':pvalue from GPTest,

'adj.pvalue':ajusted pvalues by BH method. See p.adjust.

Value

Details

This function returns the result of ABSSeq as a table or a vector depended on the given names.

See Also

ABSSeq

Examples

obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- normalFactors(obj)
obj <- calPara(obj)
obj <- GPTest(obj)
head(results(obj))
head(results(obj,c("pvalue","adj.pvalue")))