idiogramFISH (version 2.0.0)

asymmetry: FUNCTIONS asymmetry and asymmetryA2.

Description

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

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

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) (Romero-Zarco 1986)

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

(CV = coeff. var.) (Paszko 2006)

Usage

asymmetry(dfChrSize)
asymmetryA2(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

Paszko B. 2006. A critical review and a new proposal of karyotype asymmetry indices. Plant Syst Evol 258:39<U+2013>48.

See Also

chrbasicdatamono

chrbasicdatamono

chrbasicdataHolo

Examples

# NOT RUN {
asymmetry(dfOfChrSize)
myAlist<-asymmetry(bigdfOfChrSize)
as.data.frame(myAlist)
asymmetryA2(dfOfChrSize)
as.data.frame(asymmetryA2(bigdfOfChrSize))
asymmetryA2(dfChrSizeHolo)
as.data.frame(asymmetryA2(bigdfChrSizeHolo))
# }