asymmetry | R Documentation |
asymmetry: calculates karyotype asymmetry A and A2.
asymmetryA2: calculates karyotype asymmetry A2
This functions read a data.frame with columns:
shortArmSize
and longArmSize
If several species present, use
column OTU
.
It returns a list with the A and A2 indices
A = Sum (longArm - shortArm / CL) / n
A: Watanabe et al. (1999) asymmetry of karyotype ranging from 0 (symmetric) to 1 (asymmetric)
A2 = sCL / xCL
(s = std dev, CL = chr. length, x = mean) (Romero-Zarco 1986)
related to:
CVCL = A2 * 100
(CV = coeff. var.) (Paszko 2006)
asymmetry(dfChrSize, asDf = FALSE) asymmetryA2(dfChrSize)
dfChrSize |
name of data.frame |
asDf |
boolean, return d.f. instead of list |
list
Watanabe K, Yahara T, Denda T, Kosuge K. 1999. Chromosomal evolution in the genus Brachyscome (Asteraceae, Astereae): Statistical tests regarding correlation between changes in karyotype and habit using phylogenetic information. Journal of Plant Research 112: 145-161. 10.1007/PL00013869
A2: Romero-Zarco. 1986. A New Method for Estimating Karyotype Asymmetry. Taxon Vol. 35, No. 3 pp. 526-530
Paszko B. 2006. A critical review and a new proposal of karyotype asymmetry indices. Plant Syst Evol 258:39–48.
chrbasicdatamono
chrbasicdatamono
chrbasicdataHolo
asymmetry(dfOfChrSize) myAlist<-asymmetry(bigdfOfChrSize) as.data.frame(myAlist) asymmetryA2(dfOfChrSize) as.data.frame(asymmetryA2(bigdfOfChrSize)) asymmetryA2(dfChrSizeHolo) as.data.frame(asymmetryA2(bigdfChrSizeHolo))
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