Man pages for j-a-thia/genomalicious
A smorgasbord of R functions for population genomic analyses
| adegenet_DT2genX | Convert a long-format data table of genotypes into a... |
| align_many_genes_aa | Alignment of many genes (amino acid sequences) |
| align_many_genes_dna | Alignment of many genes (DNA sequences) |
| align_plot_aa | Plot amino acid alignments |
| align_plot_dna | Plot DNA alignments |
| align_rm_gaps_invars | Remove gaps and invariant sites from an alignment matrix |
| allele_counts | Calculate allele counts |
| allele_freq_corr_windows | Allele frequency correlations across genomic windows |
| allele_freqs_DT | Generate an allele frequency data table |
| allele_uniq_DT | Generate a data table of unique alleles per locus |
| amino_acid_names | Retrieve amino acid names |
| annotDT2exonList | Convert a data.table of gene annotations to a list of exon... |
| assembly_correct_gaps | Correct uneven gaps in an assembled genome |
| bayescan_inputs_pools | Generate 'bayescan' input files |
| bed2featuretab | Converts a BED file of annotations into a GenBank feature... |
| circle_cutter | Cut a replicated circular sequence to generate a linear... |
| circularity_test | Test the circularity of a genetic sequence |
| codonDT2genome | Align a codon data.table to genomic positions |
| da2DT | Convert a 'lda' object to a long-format 'data.table' |
| dadi_inputs | Genertate dadi input from genotype or allele frequency data |
| dapc_fit | Perform a DAPC of individual genotype data in a data table |
| dapc_infer | Conduct an inference of _k_ prior to DAPC. |
| dapc_plot | Plot DAPC results |
| data_FreqsMat | An example matrix of allele frequencies |
| data_Genos | An example genotype data set |
| data_PoolFreqs | An example pooled allele frequency data set |
| data_PoolInfo | An example of pool-seq sample info |
| dna2codonDT | Translate a list of coding sequences into a codon data.table |
| DT2fasta | Data table to FASTA file |
| DT2Mat_freqs | Convert a data table of allele frequencies into a matrix (or... |
| DT2Mat_genos | Convert a data table of genotypes into a matrix (or vice... |
| DT2RADdata | Convert a long-format data table into polyRAD's RADdata... |
| family_sim_compare | Compare simulated and observed inferred genetic relationships |
| family_sim_genos | Simulate families of individuals from population allele... |
| family_sim_qtl | Simulate quantitative trait from simulated families |
| fasta2DT | FASTA file to data table |
| filter_depth | Filter loci by sequencing depth |
| filter_maf | Filter loci by minor allele frequency (MAF) |
| filter_missing_loci | Filter missing data by loci |
| filter_missing_units | Filter missing data by units (sampled individuals or... |
| filter_space_loci | Filter loci based on their spacing |
| filter_supporting_reads | Filter samples by the minimum supporting reads for alleles. |
| filter_unlink | Filter for "unlinked" loci |
| fstat_calc | Calculate F-statistics from genotypes or allele frequencies... |
| fstat_varcomps | Calculate variance components for F-statistics |
| gene_map_plot | Plot a gene map |
| genomalicious | 'genomalicious': A smorgasbord of R functions for population... |
| genos2freqs | Get population allele frequencies from a (long) data table of... |
| genos2indAlleles | Convert a genotype data table to an allele data frame |
| genoscore_converter | Convert between genotype scores (separated alleles vs counts) |
| het_calc | Calculate heterozygosity from genotypes or allele frequencies |
| kmeans_join_DT | Join K-means clustering results into a reference (long)... |
| locus_overlap | Probability of random null overlap among groups for outlier... |
| miss_plot_heatmap | Plot a heatmap of missing information |
| miss_plot_hist | Plot missing genotypes, by samples |
| mitoGbk2DT | Convert a mitogenome GENBANK file into a data table |
| mitogenome_seq_repos | Reposition a mitogenomic sequence |
| mrbayes_input | Generate input file for 'MrBayes' |
| normalise_patterson | Perform the Patterson et al. (2006) normalisation to a... |
| outflank_input_freqs | Convert a (long_) allele frequency data table to 'OutFLANK'... |
| outflank_mod_fst_correct | Modificatin of OutFLANK's... |
| outflank_mod_fst_nocorrect | Modificatin of OutFLANK's... |
| pairwiseMat2DT | Convert a pairwise matrix into a pairwise data table |
| pca2DT | Convert a 'prcomp' object to a long-format 'data.table' |
| pca_genos | Perform a PCA (principal components analysis) on individual... |
| pca_plot | Plot PCA results |
| pcoa_freqs | Perform a PCoA (principal coordinates analysis) on population... |
| pcoa_plot | Plot PCoA results |
| polyrad_DT2RADdata | Convert a long-format genotype data table into polyRAD's... |
| poolfstat_DT2Fst | Calculate FST with 'poolfstat' from a data table of read... |
| poolfstat_DT2pooldata | Convert a data table of read counts into a pooldata object |
| poolne_estim_boot_pi | Parametric bootstrap of 'poolne_estim' allele frequencies |
| poolne_estim_input | Generate input files for 'poolne_estim' |
| poolne_estim_output | Merge 'poolne_estim' outputs |
| replace_miss_genos | Replace missing genotypes |
| vcf2DT | VCF file to data table |
