This function computes the relative expression profiles of all given phylostrata or divergence-strata within a given PhyloExpressionSet or DivergenceExpressionSet.

REMatrix(ExpressionSet)

Arguments

ExpressionSet

a standard PhyloExpressionSet or DivergenceExpressionSet object.

Details

For each phylostratum or divergence-stratum the corresponding relative expression profile is being computed as follows:

$$f_js = ( e_js - e_j min ) / ( e_j max - e_j min )$$

where \(e_j min\) and \(e_j max\) denote the minimum/maximum mean expression level of phylostratum j over the developmental stages s. This linear transformation corresponds to a shift by \(e_j min\) and a subsequent shrinkage by \(e_j max - e_j min\). As a result, the relative expression level \(f_js\) of developmental stage s with minimum \(e_js\) is 0, the relative expression level \(f_js\) of the developmental stage s with maximum \(e_js\) is 1, and the relative expression levels \(f_js\) of all other stages s range between 0 and 1, accordingly.

References

Domazet-Loso T and Tautz D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature (468): 815-818.

Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101.

See also

Author

Hajk-Georg Drost

Examples


# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)

# example PhyloExpressionSet
REMatrix(PhyloExpressionSetExample)
#>       Zygote  Quadrant   Globular      Heart    Torpedo       Bent    Mature
#> 1  0.4816246 0.3145330 0.46389184 0.00000000 0.17067495 0.56880234 1.0000000
#> 2  1.0000000 0.9363209 0.63348381 0.40823711 0.14904726 0.00000000 0.2206063
#> 3  0.6083424 0.4109402 0.00000000 0.09521758 0.16284114 0.21213845 1.0000000
#> 4  0.2985050 0.2366309 0.04946941 0.07499453 0.00000000 0.20573325 1.0000000
#> 5  0.2893657 0.2799777 0.00000000 0.01401191 0.01365328 0.45908792 1.0000000
#> 6  0.2323316 0.2786335 0.02706119 0.00000000 0.03592044 0.20084761 1.0000000
#> 7  0.5666979 0.2620602 0.00000000 0.12099252 0.07133814 0.13232551 1.0000000
#> 8  0.4203039 0.3092784 0.09237036 0.05442042 0.00000000 0.45520558 1.0000000
#> 9  0.4586261 0.4668613 0.39738003 0.23205534 0.00000000 0.37067096 1.0000000
#> 10 0.8811321 1.0000000 0.53841500 0.22974016 0.00000000 0.30490542 0.4881046
#> 11 0.4015809 0.4877111 0.04846721 0.05741594 0.00000000 0.07716367 1.0000000
#> 12 0.5052572 0.3359211 0.07100055 0.09489782 0.00000000 0.25811214 1.0000000

# example DivergenceExpressionSet
REMatrix(DivergenceExpressionSetExample)
#>       Zygote  Quadrant   Globular      Heart    Torpedo      Bent    Mature
#> 1  0.9669643 0.9755188 1.00000000 0.64894653 0.54294759 0.3860827 0.0000000
#> 2  0.7888009 0.4949178 0.10397567 0.00000000 0.08758660 0.4549387 1.0000000
#> 3  0.1733953 0.0000000 0.02704324 0.04893726 0.18054185 0.4309208 1.0000000
#> 4  0.3772372 0.2955661 0.08201140 0.07895260 0.00000000 0.2074848 1.0000000
#> 5  0.4543752 0.3987496 0.09292474 0.00000000 0.02050713 0.1912595 1.0000000
#> 6  0.4403615 0.2605017 0.07713944 0.13021586 0.00000000 0.2307754 1.0000000
#> 7  0.3264585 0.3200581 0.13864386 0.11077270 0.00000000 0.1420009 1.0000000
#> 8  0.4934416 0.4366671 0.11457069 0.08697865 0.00000000 0.3076689 1.0000000
#> 9  0.6236387 0.6561674 0.21851855 0.10163374 0.00000000 0.4161087 1.0000000
#> 10 0.7794318 1.0000000 0.61482564 0.22487531 0.00000000 0.1192539 0.4259882