tidypopgen0.3.2 package

An arrange method for gen_tibble objects

An arrange method for grouped gen_tibble objects

Augment data with information from a gt_pca object

Augment the loci table with information from a gt_pca object

Augment the loci table with information from a analysis object

Augment data with information from a q_matrix object

Augment data with information from a gt_dapc object

Autoplots for gt_admix objects

Autoplots for gt_cluster_pca objects

Autoplots for gt_dapc objects

Autoplots for gt_pca objects

Autoplots for gt_pcadapt objects

Autoplots for q_matrix objects

Autoplots for qc_report_indiv objects

Autoplots for qc_report_loci objects

Combine method for gt_admix objects

A $ method for gen_tibble objects

Combine a gen_tibble to a data.frame or tibble by column

Count the number of loci in a gen_tibble

Filter individuals based on a relationship threshold

Tidyverse methods for gt objects

A filter method for grouped gen_tibble objects

Find duplicates in the loci table

Constructor for a gen_tibble

Return a single P matrix from a gt_admix object

Return a single Q matrix from a gt_admix object

Add an simple feature geometry to a gen_tibble

Reorder the q matrices based on the grouping variable

Run ADMIXTURE from R

Convert a gen_tibble to a genind object from adegenet

Convert a gen_tibble to a genlight object from adegenet

Convert a gentibble to a .geno file for sNMF from the LEA package

Convert a gen_tibble to a data.frame compatible with hierfstat

Export a gen_tibble object to PLINK bed format

Convert a gen_tibble to a VCF

Find the best number of clusters based on principal components

Run K-clustering on principal components

Discriminant Analysis of Principal Components for gen_tibble

Compute and store blocked f2 statistics for ADMIXTOOLS 2

Get the names of files storing the genotypes of a gen_tibble

Checks if a gen_tibble has been imputed

Simple imputation based on allele frequencies

Imputation based XGBoost

Load a gen_tibble

Order the loci table of a gen_tibble

PCA controlling for LD for gen_tibble objects

PCA for gen_tibble objects by partial SVD

PCA for gen_tibble objects by randomized partial SVD

Principal Component Analysis for gen_tibble objects

pcadapt analysis on a gen_tibble object

Set the ploidy of a gen_tibble to include pseudohaploids

Save a gen_tibble

Sets a gen_tibble to use imputed data

Run SNMF from R in tidypopgen

Update the backing matrix

Checks if a gen_tibble uses imputed data

Estimate individual observed heterozygosity

Individual inbreeding coefficient

Estimate individual missingness

Return individual ploidy

Test if the loci table is ordered

Load example gen_tibble

Estimate allele frequencies at each locus

Get the chromosomes of loci in a gen_tibble

Test Hardy-Weinberg equilibrium at each locus

Clump loci based on a Linkage Disequilibrium threshold

Estimate missingness at each locus

Get the names of loci in a gen_tibble

Estimate nucleotide diversity (pi) at each locus

Find transitions

Find transversions

A mutate method for gen_tibble objects

A mutate method for grouped gen_tibble objects

Compute the Population Branch Statistics for each combination of popul...

Compute the Pairwise Allele Sharing Matrix for a gen_tibble object

Compute the Genomic Relationship Matrix for a gen_tibble object

Compute the Identity by State Matrix for a gen_tibble object

Compute the KING-robust Matrix for a a gen_tibble object

Compute pairwise population Fst

Pipe operator

Compute population specific FIS

Compute population specific Fst

Compute basic population global statistics

Compute the population expected heterozygosity

Compute the population observed heterozygosity

Estimate Tajima's D for the whole genome

Predict scores of a PCA

Convert a standard matrix to a q_matrix object

Create a Quality Control report for individuals

Create a Quality Control report for loci

Generate a report of what would happen to each SNP in a merge

Combine two gen_tibbles

Read and structure .Q files or existing matrices as q_matrix or `gt_...

Objects exported from other packages

Scale constructor using the distruct colours

The select_if verb for loci

The select verb for loci

Show the genotypes of a gen_tibble

Show the loci information of a gen_tibble

Show the ploidy information of a gen_tibble

Compute the Pairwise Allele Sharing Matrix for a bigSNP object

Compute the Identity by State Matrix for a bigSNP object

Compute the KING-robust Matrix for a bigSNP object

Print a summary of a merge report

Summary method for gt_admix objects

A theme to match the output of distruct

Tidy a gt_pca object

Tidy a gt_dapc object

Tidy a Q matrix

tidypopgen: Tidy Population Genetics

Detect runs of homozygosity using a sliding-window approach

Compute the Population Branch Statistics over a sliding window

Compute pairwise Fst for a sliding window

Compute Tajima's D for a sliding window

Estimate window statistics from per locus estimates