convert: convert

In oyvble/seq2lus: A MPS conversion tool from UAS sequence to LUS format

convert

Description

Sequence to LUS format converter

Usage

convert(dat, lookupf = NULL, type = "LUS", toFile = FALSE,
  outf = "converted.csv", printMissing = TRUE,
  missf = "MissingSequences.csv", LUSsymb = "_")

Arguments

dat	A data table with format [SampleName,Marker,Allele,Height] where Alleles are sequences. Height column is optional (indicating Evid if present and Ref if not present).
lookupf	The destination/path of the UAS Lookup file (use build-in by default). Must be an xlsx file with same format. Not used if LUSstrR installed
type	The convertion type (RU, LUS, LUS+)
toFile	Boolean of whether the converted data table should be saved to workspace
outf	The file name of the converted data table
printMissing	A boolean of whether alleles not found in the look-up table should be printed to a seperate file
missf	The file name of the missing alleles (not found in look-up table)
LUSsymb	The separator format to use.

Details

This script enables users to provide their own UAS sequence data and convert the sequences directly to different formats. The formats supported are RU (Repeat Unit/CE), LUS (Longest Uninterupted Stretch), LUS+ (extended version of LUS), or STRseq (The short format provided by STRseq) The lookup table was created by Rebecca Just. The converter can also utilize LUSstrR if installed

Value

Returning a table with format [SampleName,Marker,Allele,Height]

Author(s)

Oyvind Bleka (in collaboration with Rebecca Just)

oyvble/seq2lus documentation built on March 21, 2022, 11:01 p.m.