monomorphic: Set monomorphic sites to freq =1

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

Description

In our analysis we calculate frequencies prior to removing false positives. Sometimes this means we have a monomorphic site with the allele present at <100 in each case this holds true. That work is in 2017_11_13.Rmd- 2017_11_16.Rmd in the notebook directory of the HIVE repo. It is also true we will miss some true variants in the <10 frequenies of 1.

Usage

monomorphic(df, ...)

Arguments

df	variant data frame
...	columns to group by. There's no current need for them to be anything but SPECID,season,chr,pos,pcr_result

Value

the input data frame but with monomorphic frequencies = 1.

Examples

wacky_isnv<-small_isnv
wacky_isnv$freq.var[wacky_isnv$mutation=="PB2_G1602A"]<-0.8
monomorphic(wacky_isnv,SPECID,season,chr,pos,pcr_result)

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