bind_data_multiallelic: Bind multi-allelic format data to project

In bobverity/MALECOT: Joint estimation of COI and population structure for malaria genetic data

Description

Bind data in multi-allelic format to MALECOT project. Data should be formatted as a dataframe with three columns: "sample_ID", "locus" and "haplotype". Each row of this dataframe specifies a haplotype that was observed at that locus in that individual. Haplotypes should be coded as positive integers.

Usage

bind_data_multiallelic(project, df, pop = NULL, missing_data = -9,
  alleles = NULL, name = NULL, check_delete_output = TRUE)

Arguments

project	a MALECOT project, as produced by the function malecot_project()
df	a dataframe with three columns, as decribed above
pop	ostensible populations of the samples
missing_data	what value represents missing data. Defaults to -9. Must be a positive or negative integer
alleles	the number of alleles at each locus. If scalar then the same number of alleles is assumed at all loci. If NULL then the number of alleles is inferred directly from data as the maximum observed value per locus
name	optional name of the data set to aid in record keeping
check_delete_output	whether to prompt the user before overwriting existing data

Examples

# TODO

bobverity/MALECOT documentation built on May 13, 2019, 4:01 a.m.