bind_data_biallelic: Bind bi-allelic data to project

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

Description

Bind data in bi-allelic format to MALECOT project. Data should be formatted as a dataframe with samples in rows and loci in columns. Genetic data should be coded as 1 (homozygote REF allele), 0 (homozygote ALT allele), or 0.5 (heterozygote). Additional meta-data columns can be specified, including a column for sample IDs and a column for sampling population.

Usage

bind_data_biallelic(project, df, ID_col = 1, pop_col = NULL,
  data_cols = NULL, ID = NULL, pop = NULL, missing_data = -9,
  name = NULL, check_delete_output = TRUE)

Arguments

project	a MALECOT project, as produced by the function malecot_project()
df	a dataframe containing genetic information and optional meta-data
ID_col	which column of the input data contains the sample IDs. If NULL then IDs must be defined seperately through the ID argument
pop_col	which column of the input data contains the ostensible population of the samples. If NULL then populations must be defined seperately through the pop argument
data_cols	which columns of the input data contain genetic information. Defaults to all remaining columns of the data once meta-data columns have been accounted for
ID	sample IDs. Ignored if using the ID_col option
pop	ostensible populations. Ignored if using the pop_col option
missing_data	what value represents missing data. Defaults to -9. Must be a positive or negative integer, and cannot equal 0 or 1 as these are reserved for genetic data.
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.