README.md

In pygmyperch/melfuR: A collection of ugly R functions for analysis of SNP and spatial data.

http://www.molecularecology.flinders.edu.au/            Chris Brauer     

melfuR

A collection of ugly R scripts for exploratory analysis of ddRAD data, spatial analyses and other (hopefully) useful utilities.

These are mostly just wrapper scripts to simplify running basic pop-gen analyses using a single format (adegenet: genind) \ The code is characteristically ugly :dizzy_face: but feel free to use/modify whatever you find useful

How to Install

The preferred way to install this package is using devtools:

First install devtools

install.packages("devtools")

Then install melfuR

devtools::install_github("pygmyperch/melfuR")

A quick overview of the functions:

• rainbow.genind: an example genind object consisting of 500 loci and 249 individuals from 14 populations of Melanotaenia fluviatilis in the Murray-Darling Basin.

• rainbow.env: environmental data for 14 populations of Melanotaenia fluviatilis in the Murray-Darling Basin.

• DelphinusXY: XY coordinates of common dolphin Delphinus delphis sampling locations in Australia and New Zealand.

• MDB_cols: custom color palette based on the Murray-Darling Basin landscape.

• view_colors: view the MDB color palette.

• expand_pop2ind: expands population-level metadata to an individual-level data frame.

• HWE_filter: filter loci for HWE by population using a genind object

• impute_genotypes: impute missing genotypes in a genind or genlight object using population allele frequencies estimated with Sparse Non-Negative Matrix Factorization (LEA::snmf).

• sort_alleles: sort alleles in a genind or genlight object based major/minor status, optionally sort relative to a specified reference population.

• percent_poly: calculate the % polymorphic loci per population from a genind object

• diversity_stats: calculate basic genetic diversity stats from a genind object

• missing_data: calculate the % of missing genotypes per population from a genind object

• subset_snps: subset a structure file based on a list of loci

• viamaris: calculate pairwise oceanic distances from a set of XY coordinates.

• extract_tri: extract upper or lower triangle from a square matrix.

• sf2KML: convert sf points, lines, and polygon objects to .kml files.

• clean_vcf_INFO: clean-up INFO fields in a VCF file to remove any fields not present across all records.

• polarise_ancestral_vcf: polarise a VCF file setting the (supplied) ancestral allele as REF.

• manage_files: perform file operations such as listing, copying, and moving files.

• write_list_to_excel: write a list of data frames to an Excel file (.xlsx).

pygmyperch/melfuR documentation built on Aug. 26, 2024, 12:48 a.m.