results: Accessor functions for the result from a ABSDataSet

In ABSSeq: ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences

Description

Accessor functions for the result from a ABSDataSet by given names

Usage

## S4 method for signature 'ABSDataSet'
results(object, cnames = c("Amean", "Bmean",
  "baseMean", "absD", "Variance", "rawFC", "lowFC", "foldChange", "pvalue",
  "adj.pvalue", "trimmed"))

Arguments

object

a ABSDataSet

cnames

a vecotr of names for output, which are among: 'Amean','Bmean', log2 of mean counts for group A and B, "baseMean', estimated mean for absolute counts difference (absD), used for mu in pnbinom 'absD', absolute counts difference in total 'Variance', pooled Variance for two groups 'rawFC','lowFC', 'foldChange', log2 fold-change of original (Bmean-Amean), corrected by expression level and corrected by both expression level and gene-specific dispersion 'pvalue','adj.pvalue', pvalue and adjusted pvalue 'trimmed', number of trimmed outliers

Details

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

Value

a table according to canmes.

See Also

ABSSeq

Examples

data(simuN5)
obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- normalFactors(obj)
obj <- callParameter(obj)
obj <- callDEs(obj)
head(results(obj))

Example output

Normalizing used qtotal!
      Amean     Bmean    baseMean  absD     Variance      rawFC      lowFC
1  3.557138  3.347798    61.52524    25 1.174319e+03 -0.2093404 -0.1146444
2 10.654283 13.551314 23458.65032 84079 5.006097e+08  2.8970309  2.6628526
3 11.056413 13.037606  5524.26166 10567 1.904550e+06  1.9811932  0.9029868
4  4.097485  4.961327   114.26121   209 5.895087e+03  0.8638418  0.5941570
5 11.543451 13.760796 18263.75752 55896 1.884588e+07  2.2173452  2.1036125
6  9.196377 10.353267  1771.36352  2942 2.371328e+05  1.1568894  0.9863872
   foldChange       pvalue adj.pvalue trimmed
1 -0.04566872 7.449780e-01 1.00000000       0
2  0.35171829 4.419554e-02 1.00000000       0
3  0.52921978 2.124437e-02 0.81191274       2
4  0.20714118 1.528670e-01 1.00000000       0
5  1.01251221 5.787243e-05 0.01602295       0
6  0.43788761 6.973058e-02 1.00000000       0

ABSSeq documentation built on Nov. 8, 2020, 5:07 p.m.