callAllele: Automatically call or flag alleles from NGS data

Description Usage Arguments Details Value

View source: R/callAllele.R

Description

Call or flag candidate alleles to construct a consensus genotype.

Usage

1
callAllele(fb, tbase = NULL, clean = TRUE, verbose = FALSE)

Arguments

fb

A fishbone object.

tbase

A data.frame with thresholds which are locus specific. Thresholds are:

  • stutter (if lower than this, allele is ignored as stutter)

  • disbalance (if heterozygous alleles are not in 1:1 ratio)

  • low count (anything below this threshold gets flagged as light on read count)

  • allele with no stutter height (if no stutter is found, how many reads do we allow for alleles to be called)

clean

Logical. If TRUE (default), it will return only called alleles and their stutters.

verbose

Logical. If TRUE, it will print which sample is being processed.

Details

Function works on an individual run (one PCR reaction). Apply this to sample * locus * run combination. The data should come from an NGS run as processed by de Barba et al. (2016).

For algorithm used to find stutters, see findStutter.

De Barba, M., Miquel, C., Lobréaux, S., Quenette, P. Y., Swenson, J. E., & Taberlet, P. (2016). High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA. Molecular Ecology Resources, 1-16. https://doi.org/10.1111/1755-0998.12594

Key for abbreviations used in (pseudo)code:

The result is appended three columns; one for called A, one for flagged alleles and if read is a stutter. Possible flags are:

Algorithm is as follows:

Value

Output should be all alleles and their stutters.


romunov/fishbone documentation built on Nov. 3, 2018, 8:28 p.m.