hapfreq_from_paper: Find instances where all accessions from one paper are unique...

In EvolEcolGroup/mtDNAcombine: R package to download, combine, and curate sequences from public databases

Description

hapfreq_from_paper

Usage

hapfreq_from_paper(freq_by_study, new_rownam, max_haps_found_together)

Arguments

freq_by_study	matrix created by haploFreq function (pegas) using categorical variable formed of first 5 characters of accession number.
new_rownam	character string of accession versions with first five characters repeated and pasted with an underscore in front of full string to create a two part row name ID
max_haps_found_together	Threshold value for number of times a haplotype can be found repeated in the uploads from one study before paper is assumed to have submitted ever sample rather than unique haplotypes.

Details

This function finds the associated paper in instances where every accession from one study represents a novel haplotype, likely indicating data is not at sampled frequency.

Where every accession is a novel haplotype for the given species/gene this function finds the associated paper. In such instances the original paper will need to be read to find values to multiple haplotypes by in order to reach original sampled frequency.

EvolEcolGroup/mtDNAcombine documentation built on July 8, 2021, 10:30 p.m.