summarize_trans_compl: Summarize results obtained with phyloscanner.

View source: R/summary_utils.R

summarize_trans_complR Documentation

Summarize results obtained with phyloscanner.

Description

Summarize results obtained with phyloscanner.

Usage

summarize_trans_compl(data)

Arguments

data

Details

Here we summarized the results obtained with phyloscanner. The summary is based on the summary results that phyloscanner returns in which it summarizes the "ancestry" type by window. We considered that two individuals are linked if proportion of values for ancestry is complex, multiTrans and trans are >= 0.50 On the other hand, we considered that two individuals represent a true direction of transmission from host.1 to host.2 if the proportion of multiTrans, trans, and complex are >= 0.375. Here, we are interested to understand whether including complex transmissions would make it better to detect direction of transmission. Note that to carry out this summary, we pre-removed all ancestry = noAncestry.

Value

Dataframe containing information of whether host.1 and host.2 are linked and whether there direction of transmission is also correct.


thednainus/HIVepisimAnalysis documentation built on Sept. 21, 2023, 7:32 a.m.