summarize_trans: Summarize results obtained with phyloscanner.

In thednainus/HIVepisimAnalysis: Functions to analyse results from network analysis

Summarize results obtained with phyloscanner.

Description

Summarize results obtained with phyloscanner.

Usage

summarize_trans(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 and trans are >= 0.375. These cut-off values were based on Zhang et al.Clin Infect Dis. 2021 Jan 1; 72(1): 30–37. 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.