# Tidy Multilocus Amplicon Genotypes

## Documentation for package ‘tidyGenR’ version 0.1.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

add_allele_no | add allele_no to genotypes
amplisas2tidy | Read AmpliSAT results into tidy variants
check1_lowcount | Check1
check2_unique_snames | Check2
check3_non_orphan | Check3
check_raw_reads | Check input raw FASTA/Q files
chimera_removal | Variant calling using DADA2 ASV approach
compare_calls | Comparision between multiple tidy variants or genotypes.
cutadapt_command | Create cutadapt command
dada2list | Variant calling using DADA2 ASV approach
demultiplex | Demultiplex reads by locus
dereplicate | De-replicate reads into frequency tables for a set of FASTQ files
dist_m | Distance between two matrices
dist_m_all | Applies distance between all tables in a list.
explore_dada | Explore variants output by DADA2 in the parameter space
filter_variants | Filter variants based on frequency and depth
genotype | Genotype samples from tidy variants
genotypes | Genotypes
genotype_conversion | Conversion among genotype formats: tidy, compact, wide, STRUCTURE
geno_direct | Genotype samples from tidy variants
gen_compact2wide | Conversion among genotype formats: tidy, compact, wide, STRUCTURE
gen_tidy2compact | Conversion among genotype formats: tidy, compact, wide, STRUCTURE
gen_tidy2genalex | Conversion among genotype formats: tidy, compact, wide, STRUCTURE
gen_tidy2integers | Conversion among genotype formats: tidy, compact, wide, STRUCTURE
gen_tidy2wide | Conversion among genotype formats: tidy, compact, wide, STRUCTURE
gen_wide2structure | Conversion among genotype formats: tidy, compact, wide, STRUCTURE
loess_err_mod4 | Variant calling using DADA2 ASV approach
mds_comp | plot MDS
out_popart | Format MSA and traits for PopArt
primers | Primers for multiplex PCR
reads_loci_samples | Output reads per locus
reads_track | Output reads across pipeline
remove_hemizygotes | Remove hemizygote calls
remove_monomorphic | Remove monorphic loci
remove_poor_fastq | Remove empty FASTQ
rename_alleles | Rename alleles in a dataframe based on reference alleles
rm_n_msa | Remove Ns introduced in 'mergePairs(justConcatenate = T)'
tidy2sequences | Output FASTA sequences
truncate | Truncate reads
trunc_amp | Truncate reads
trunc_fr | Per-locus truncation lengths for forward and reverse reads.
variants | Variants
variant_call | Variant calling
variant_calling_dada | Variant calling using DADA2 ASV approach
variant_calls | List of tidy variants
variant_call_dada | Variant calling using DADA2 ASV approach
var_seq2len | Convert sequence-based variants to length-based