threshs: Customizing thresholds

In Fragman: Fragment Analysis in R

Customizing thresholds

Description

This function takes data contained in a list with 2 elements, the first containing the position in base pairs and the heights of the positions and given a panel finds the best minimum threshold by creating a confidence interval in order to get only the real peaks. Implemented internally of auto,score and score.easy function.

Usage

threshs(my.plant, min.thre=200, panel, ci=1.9)

Arguments

my.plant	List with 2 elements; the position in base pairs and the heights associated with them
min.thre	Starting threshold to find the peaks and refine the search
panel	Two scalar values indicatin the interval where the peaks should be found
ci	Scalar value indicating the number of standard errors to be used when creating the confidence interval for ssr calling

Details

No major details.

Value

If arguments are correctly specified the function returns a list containing

$newthre

A scalar value indicating the new threshold to be used when calling the real peaks

References

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

data(my.plants)
# implemented internally of auto,score and score.easy function
# threshs(my.plant, min.thre=200, panel=(260,290), ci=1.9)

Fragman documentation built on May 24, 2026, 5:08 p.m.