sangergenotype: A function to interpret genotype information from ab1 files

In moritzlindner/mousecolonytools: A collection of tools to facilitate genotyping and mouse colony management

A function to interpret genotype information from ab1 files

Description

This function retrieves ab1 files either from a link or from a directory and compares the sequence to a reference sequence. it interprets signal amplitudes in abi traces and can thereby fidderentiate between wt, hom and het.

Usage

sangergenotype(
  dir = choose.dir(),
  link = "",
  wtseq = "",
  mutseq = "",
  revcomp = TRUE,
  cutoff = 0.33,
  pattern = "K[0-9]{4}+"
)

Arguments

dir	Source directory for .ab1 files to analyze or, if link is not blank, directory where to download and unpack the archive containing .ab1 files to. In that case, a new subdirectory named by the current date will be created. If left blank, a file open dialog will appear.
link	Optional. A url to an archive containing the ab1 files to analyze.
wtseq	Sequence snipplet caracteristic for wild-type
mutseq	Sequence snipplet caracteristic for mutant
revcomp	make reverse complementary of wtseq and mutseq
cutoff	minimum relative amplitude of secondary peak. This is the threshold for interpreting a double peak as heterozygous.
pattern	A regular expression that matches a unique pattern in the file name (like the mouse name). Could be e.g. "K[0-9]{4}+" or "[0-9]{1,2}_[0-9]{1,2}[a-z]{1}+".

Value

Data Frame with list of mice and respective genotypes

Examples

## Not run: 
sangergenotype(dir="D:\\", link="http://www.x.zip",wtseq="ACTGAAAA",mutseq="ACCGAAAA", revcomp = TRUE, cutoff = 0.2)

## End(Not run) 

moritzlindner/mousecolonytools documentation built on Aug. 6, 2023, 6:45 a.m.