This function computes the LateConservationTest score for a given TAI
or TDI pattern.
The reductive late 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_early - T_late and D2 = T_mid - T_late are calculated.
- The minimum D_min of D1 and D2 is computed as final test statistic of the reductive late conservation test.
This function lcScore computes the D_min value for a given TAI or TDI
stored in the age_vals argument.
lcScore(age_vals, early, mid, late, profile.warn = FALSE)a numeric vector containing TAI or TDI values for each developmental stage s.
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 boolean value indicating whether a warning is printed when a high-mid-low pattern isn't followed.
a numeric value representing the late conservation score.
# read standard phylotranscriptomics data
data(PhyloExpressionSetExample)
data(DivergenceExpressionSetExample)
# Example PhyloExpressionSet:
# compute the TAI profile
TAIs <- TAI(PhyloExpressionSetExample)
# compute the late conservation score for the TAI profile
lc_score <- lcScore(age_vals = TAIs,early = 1:2,mid = 3:5,late = 6:7)
# Example DivergenceExpressionSet:
# compute the TDI profile
TDIs <- TDI(DivergenceExpressionSetExample)
# compute the late conservation score for the TDI profile
lc_score <- lcScore(age_vals = TDIs,early = 1:2,mid = 3:5,late = 6:7)
# compute lcScore() vector from bootMatrix()
apply(bootMatrix(PhyloExpressionSetExample,10),1,lcScore,early = 1:2,mid = 3:5,late = 6:7)
#> 1 2 3 4 5 6
#> -0.035975502 -0.037154844 -0.023278212 -0.051900074 -0.016272788 0.034063484
#> 7 8 9 10
#> 0.032440418 0.004459241 -0.077836247 -0.037626594
# get warning if the expected pattern isn't followed
lc_score <- lcScore(age_vals = TAIs,early = 1:2,mid = 3:5,late = 6:7,profile.warn=TRUE)
#> The phylotranscriptomic pattern may not follow a late conservation pattern (high-mid-low or high-high-low).