This function computes the EarlyConservationTest score for a given
The reductive early conservation test is a permutation test based on the following test statistic.
- A set of developmental stages is partitioned into three modules - early, mid, and late - based on prior biological knowledge.
- The mean
TDI value for each of the three modules T_early, T_mid, and T_late are computed.
- The two differences D1 = T_mid - T_early and D2 = T_late - T_early are calculated.
- The minimum D_min of D1 and D2 is computed as final test statistic of the reductive hourglass test.
This function ecScore computes the D_min value for a given
stored in the
ecScore(age_vals, early, mid, late)
a numeric vector containing
a numeric vector storing the numeric stage values that correspond to the early phase of development.
a numeric vector storing the numeric stage values that correspond to the middle phase of development.
a numeric vector storing the numeric stage values that correspond to the late phase of development.
a numeric value representing the early conservation score.
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# read standard phylotranscriptomics data data(PhyloExpressionSetExample) data(DivergenceExpressionSetExample) # Example PhyloExpressionSet: # compute the TAI profile TAIs <- TAI(PhyloExpressionSetExample) # compute the early conservation score for the TAI profile ec_score <- ecScore(age_vals = TAIs,early = 1:2,mid = 3:5,late = 6:7) # Example DivergenceExpressionSet: # compute the TDI profile TDIs <- TDI(DivergenceExpressionSetExample) # compute the early conservation score for the TDI profile ec_score <- ecScore(age_vals = TDIs,early = 1:2,mid = 3:5,late = 6:7) # compute ecScore() vector from bootMatrix() apply(bootMatrix(PhyloExpressionSetExample,10),1,ecScore,early = 1:2,mid = 3:5,late = 6:7)