idiogramFISH (version 1.12.1)

asymmetry: FUNCTION to calculate karyotype asymmetry A and A2

Description

This function reads 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

$$A = \frac{\sum_{i=1}^{n} \frac{longArm_{i} - shortArm_{i}}{CL_{i}} }{n} $$

A: Watanabe et al. (1999) asymmetry of karyotype ranging from 0 (symmetric) to 1 (asymmetric) $$A_{2} = \frac{sCL}{xCL}$$

(s = std dev, CL = chr. length, x = mean)

related to: $$CV_{CL} = A_{2} * 100$$

(CV = coeff. var.)

Usage

asymmetry(dfChrSize)

Arguments

dfChrSize

name of data.frame

Value

list

References

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

See Also

chrbasicdatamono

Examples

# NOT RUN {
asymmetry(dfOfChrSize)
myAlist<-asymmetry(bigdfOfChrSize)
as.data.frame(myAlist)
# }