threshs

List with 2 elements; the position in base pairs and the heights associated with them

my.plant

Starting threshold to find the peaks and refine the search

min.thre

Two scalar values indicatin the interval where the peaks should be found

panel

Scalar value indicating the number of standard errors to be used when creating the confidence interval for ssr calling

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.

Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file and contains DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).

threshs: Customizing thresholds

Description

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Examples