letter.to.jm: Letter to JoinMap code converter

In Fragman: Fragment Analysis in R

Description

This function converts a vector of ssr calls in letter format to joinmap code using information from mother and father provided in first and second row respectively

Usage

letter.to.jm(x)

Arguments

x	A vector of ssr calls in letter format or snp types, mother and father of the population should be in 1st and 2nd position respectively

Details

If numeric data exists first needs to be converted to letter code in order to use this function.

Value

If arguments are correct the function returns a list containing

$y

A vector with ssr calls in joinmap format

References

Covarrubias-Pazaran G, Diaz-Garcia L, Schlautman B, Salazar W, Zalapa J. Fragman: An R package for fragment analysis. 2016. BMC Genetics 17(62):1-8.

Robert J. Henry. 2013. Molecular Markers in Plants. Wiley-Blackwell. ISBN 978-0-470-95951-0.

Ben Hui Liu. 1998. Statistical Genomics. CRC Press LLC. ISBN 0-8493-3166-8.

Examples

xx <- data.frame(cbind(a=rep(150, 96), b=c(rep(100,48), rep(150,48))))
xx1 <- num.to.lett(xx)
letter.to.jm(unlist(xx1))
# try using apply to a dataframe

Example output

 [1] "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm"
[16] "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm"
[31] "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm" "lm"
[46] "lm" "lm" "lm" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll"
[61] "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll"
[76] "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll" "ll"
[91] "ll" "ll" "ll" "ll" "ll" "ll"

Fragman documentation built on May 2, 2019, 8:26 a.m.