ecScore {myTAI} | R Documentation |
Compute the Hourglass Score for the EarlyConservationTest
Description
This function computes the EarlyConservationTest score for a given TAI
or TDI
pattern.
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 TAI
or 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 TAI
or TDI
stored in the age_vals
argument.
Usage
ecScore(age_vals, early, mid, late)
Arguments
age_vals |
a numeric vector containing |
early |
a numeric vector storing the numeric stage values that correspond to the early phase of development. |
mid |
a numeric vector storing the numeric stage values that correspond to the middle phase of development. |
late |
a numeric vector storing the numeric stage values that correspond to the late phase of development. |
Value
a numeric value representing the early conservation score.
Author(s)
Hajk-Georg Drost
See Also
EarlyConservationTest
, TAI
, TDI
Examples
# 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)