PopPsiSeqR (version 1.0.0)

import.freqtbl: Load Merged Allele Frequency Table

Description

This function accepts as input a path to a BED file containing allele frequency and returns a GRanges object ready for the freqShifter function.

Usage

import.freqtbl(freqtbl_filename)

Value

frequency table as bedgraph

Arguments

freqtbl_filename

file containing the allele frequencies as an extended BED6+ file

input format

This function accepts as input a path to a file in an extended BED6+ format; specifically,

`chrom start end name score strand reference_allele alternate_allele selected_parent_count selected_parent_allele_frequency backcrossed_parent_count backcrossed_parent_allele_frequency offspring_count offspring_allele_frequency`

eg,

`chr2L 8517 8518 0 0 + G A 8 0 16 0.25 8 0.25`

Some of these fields (name, score, strand, reference_allele, alternate_allele, selected_parent_count, backcrossed_parent_count, offspring_count) are required as placeholders but not used in the current PopPsiSeq algorithm This format is the output of joining and filtering the output of vcftools' --freq output; see vignette for details

Examples

# \donttest{
merged_frequencies.filename <- system.file("extdata",
"merged_frequencies.example_data.tbl", package = "PopPsiSeqR")
frequencies.bg <- import.freqtbl(merged_frequencies.filename)
# }