Differential Expression accessor for a CeTF class object.

The DE accessor access the differential expression resulted from runAnalysis function analysis.

getDE(x, type = "unique")

# S4 method for CeTF
getDE(x, type = "unique")

Arguments

x	CeTF-class object
type	Type of DE matrix: unique and all (default: unique)

Value

Returns the DE genes with the statistics.

See also

runAnalysis.

Examples

# load the CeTF class object resulted from runAnalysis function
data(CeTFdemo)

getDE(CeTFdemo)
#>                     cond1     cond2       diff
#> ENSG00000004799 3.3509148  5.732294  -5.389919
#> ENSG00000013293 4.3720462  1.832860   5.606028
#> ENSG00000096060 3.9058395  7.764118  -8.690335
#> ENSG00000099337 2.8457597  5.284203  -5.517441
#> ENSG00000101347 6.3098876  9.977244  -8.263684
#> ENSG00000102760 3.5147919  6.116201  -5.881619
#> ENSG00000103196 5.3315203  7.848012  -5.691855
#> ENSG00000105989 4.4014162  1.825516   5.688073
#> ENSG00000109906 0.3189303  5.064960 -10.674185
#> ENSG00000112936 4.0678752  7.117120  -6.882394
#> ENSG00000116285 5.6009746  7.920472  -5.251633
#> ENSG00000120129 5.2475865  8.081747  -6.401746
#> ENSG00000123610 4.6209629  2.281824   5.158985
#> ENSG00000124766 6.6902518  4.254320   5.375287
#> ENSG00000127954 0.7102152  4.282559  -8.051358
#> ENSG00000128606 6.3782942  3.988086   5.273109
#> ENSG00000135821 7.7075018 10.537674  -6.392833
#> ENSG00000136999 5.1218386  2.687683   5.371317
#> ENSG00000138316 6.0255217  3.537128   5.492523
#> ENSG00000143127 1.3318644  4.294116  -6.687990
#> ENSG00000146250 4.6994960  2.176922   5.568905
#> ENSG00000152583 2.2506851  6.431200  -9.410435
#> ENSG00000154734 8.8804685 11.142348  -5.122875
#> ENSG00000157514 4.3092213  7.343255  -6.848401
#> ENSG00000162692 5.5072796  2.081457   7.587388
#> ENSG00000163083 1.9179108  4.839745  -6.597670
#> ENSG00000163884 1.6310303  5.453959  -8.611340
#> ENSG00000165072 3.1083909  5.507955  -5.430558
#> ENSG00000165995 2.3899140  5.317903  -6.611425
#> ENSG00000167641 1.7920469  4.171263  -5.385085
#> ENSG00000170214 1.1186220  4.156640  -6.857304
#> ENSG00000171819 0.4782056  3.290682  -6.353289
#> ENSG00000178695 7.7634215  5.183932   5.696093
#> ENSG00000179094 3.0474487  5.998701  -6.663410
#> ENSG00000189221 4.3818217  7.596429  -7.251928
#> ENSG00000198624 4.5604851  7.346041  -6.293129
#> ENSG00000211445 6.2677944  9.897928  -8.180500
#> ENSG00000214814 4.2359828  1.632751   5.749151
#> ENSG00000221866 3.1309547  5.629822  -5.652469