get_freqs: Get and compare the frequencies of mutations in two samples.

In jtmccr1/HIVEr: Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort

Description

This function compares the frequencies of alleles found in two samples. It relies on equal_compare to make fair comaparisons at each loci.

Usage

get_freqs(pairs, snv)

Arguments

pairs	A vector of SPECID. These strings must be found in the SPECID column of the iSNV data frame
snv	A data frame of isnv calls from deepSNV with a SPECID column

Value

a data frame with a row for each allele that differs between the two samples. Each loci that differs should have two rows (one for each allele). If there are no iSNV or none that differ then an empty data frame is returned.

See Also

equal_compare

Examples

# There  one shared iSNV here and one fixed difference the rest are the same.
print(small_isnv)
get_freqs(c("HS1595","HS1563"),small_isnv)

jtmccr1/HIVEr documentation built on May 29, 2019, 1:50 a.m.