processEigenstrat {BREADR}

process Eigenstrat data

Description

A function that takes paths to an eigenstrat trio (ind, snp and geno file) and returns the pairwise mismatch rate for all pairs on a thinned set of SNPs. Options include choosing thinning parameter, subsetting by population names, and filtering out SNPs for which deamination is possible.

Usage

processEigenstrat(
  indfile,
  genofile,
  snpfile,
  filter_length = NULL,
  pop_pattern = NULL,
  filter_deam = FALSE,
  outfile = NULL,
  chromosomes = NULL,
  verbose = TRUE
)

Arguments

indfile

path to eigenstrat ind file

genofile

path to eigenstrat geno file.

snpfile

path to eigenstrat snp file.

filter_length

the minimum distance between sites to be compared (to reduce the effect of LD).

pop_pattern

a character vector of population names to filter the ind file if only some populations are to compared.

filter_deam

a TRUE/FALSE for if C->T and G->A sites should be ignored.

outfile

(OPTIONAL) a path and filename to which we can save the output of the function as a TSV, if NULL, no back up saved. If no outfile, then a tibble is returned.

chromosomes

the chromosome to filter the data on.

verbose

controls printing of messages to console

Value

out_tibble: A tibble containing four columns:

Examples

# Use internal files to the package as an example
indfile <- system.file("extdata", "example.ind.txt", package = "BREADR")
genofile <- system.file("extdata", "example.geno.txt", package = "BREADR")
snpfile <- system.file("extdata", "example.snp.txt", package = "BREADR")
processEigenstrat(
indfile, genofile, snpfile,
filter_length=1e5,
pop_pattern=NULL,
filter_deam=FALSE
)