mhap_transform: Transform long genos to different formats for downstream...

In eriqande/microhaplotopia: Tools for Working with Microhaplot Data a la the SWFSC

Description

Takes a long genotype dataframe and transforms it to be the initial format required for different genetic analysis programs. Current options for genetic analysis programs include: CKMRsim, rubias, snppit(?), franz(?), adegenet, structure (?), WHAT ELSE DO PEOPLE COMMONLY USE HERE.... The 2columnformat_haplotype is a standard wide dataframe that has 2 columns per locus with 1 row per sample. Missing data is coded as NA The 2columnformat_numeric has haplotypes coded as integers, it returns a list of dataframes, the first being the 2 column format named 'data', and the second dataframe (named 'key') is the key for haplotype to integer conversion done within the function. The 'adegenet_2col' produces a dataframe to be passed into 'adegenet::df2genind'

Usage

mhap_transform(long_genos, program, metadata = NULL)

Arguments

long_genos	dataframe of filtered haplotypes. This is the output from the "filter_raw_microhap_data" function.
program	The program you want to create an input file for. This could be 'CKMRsim', 'rubias', 'franz', '2columnformat_haplotype', '2columnformat_numeric', 'adegenet_2col'ADD OTHERS HERE.
metadata	Not required. If supplied, metadata will be joined to genotype data before the output file is written. For franz, metadata must be in the following order: indiv.ID, birth_year, death_year, sex. Sex is M, F or ? (for unknown). For rubias, metadata is in the following order: indiv.ID, sample_type, repunit, collection (for details see 'vignette("rubias-overview")')

eriqande/microhaplotopia documentation built on July 7, 2020, 1:16 a.m.