genotypetools: A package to accelerate interpretation of sanger sequencing based genotyping results in R

Project page on github.

Installation

if (!requireNamespace("remotes", quietly = TRUE)){
  install.packages("remotes")
}
remotes::install_github("moritzlindner/genotypetools")

Description

The main function of this package is \code{sangergenotype()}. It takes a directory or a url to a zip file, cycles through all ab1 files therein and compares the traces to provided reference sequences for wt and mutant alleles. Based on thresholding it can discriminate between wt, het, and hom. Results are returned in a data frame. There are several additional functions which can be helpful when visualizing sanger genotyping data.

Examples

Example 1:

library(genotypetools)

sangergenotype(dir="D:\\", link="http://www.x.zip",wtseq="ACTGAAAA",mutseq="ACCGAAAA", revcomp = TRUE, cutoff = 0.2)
as.data.frame(tmp) 

Developed by Moritz Lindner