Tidy Multilocus Amplicon Genotypes

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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