diverse_sites: Get sites with diverisity

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

Description

In our analysis we are not interested in loci that only have one allele present within a season. Cutting out such loci helps focus on the important loci and distinctions between samples. This function counts the unique "var" entries in a dataframe according to the set grouping and removes sites that don't meet the cut off.

Usage

diverse_sites(df, cutoff, ...)

Arguments

df	variant data frame
cutoff	integer. The allele must be found more than this many times in the groupings below.
...	columns to group by. There's no current need for them to be anything but season,chr,pos,pcr_result as this allows us to

Value

the input data frame but with sites with more alleles than the cut off

Examples

diverse_sites(small_isnv,1,season,pcr_result,pos,chr)

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