README.md

In labroo2/deStructure: An S3 Class to work with structure files

deStructure

This repository holds the R package deStructure, which facilitates working with the program STRUCTURE (Pritchard et al., 2003). Scripts which process STRUCTURE output have only been optimized for the ADMIXTURE model with the flags below, i.e. no use of the POPINFO flag or MAPDISTANCES, etc.

This package, deStructure, has 6 functions:

• deStruct - Parses structure output files and stores information in a S3 class object

• average_runs - Averages across replications of STRUCTURE for a given value of K. Note that in this implementation, the user must ensure that the clusters are in a consistent order for the input.

• structure_plot - Visualize individual allele ancestries, to delineate the likely level of population subdivision

• mainparams -This functions generates the mainparams file needed for the program STRUCTURE v 2.3.

• extraparams - This functions generates the extraparams file needed for the program STRUCTURE v 2.3.

• structure_scriptwriter - This function writes scripts suitable for running STRUCTURE on a UNIX-based high-performance computing cluster up to a given number of populations and replications

Parameters for which output parsing was optimized:

define LABEL 1

define POPDATA 0

define POPFLAG 0

define LOCDATA 0

define PHENOTYPE 0

define MARKERNAMES 1

define MAPDISTANCES 0

define ONEROWPERIND 0

define PHASEINFO 0

define PHASED 0

define RECESSIVEALLELES 0

define EXTRACOLS 0

define MISSING -9

define PLOIDY 2

define MAXPOPS 1

define BURNIN 10000

define NUMREPS 50000

define NOADMIX 0

define LINKAGE 0

define USEPOPINFO 0

define LOCPRIOR 0

define INFERALPHA 1

define ALPHA 1.0

define POPALPHAS 0

define UNIFPRIORALPHA 1

define ALPHAMAX 10.0

define ALPHAPROPSD 0.025

define FREQSCORR 1

define ONEFST 0

define FPRIORMEAN 0.01

define FPRIORSD 0.05

define INFERLAMBDA 0

define LAMBDA 1.0

define COMPUTEPROB 1

define PFROMPOPFLAGONLY 0

define ANCESTDIST 0

define STARTATPOPINFO 0

define METROFREQ 10

define UPDATEFREQ 1

labroo2/deStructure documentation built on May 8, 2019, 8:58 p.m.