sv.summary.interactive: Interactive summary of the calls

In jmonlong/PopSV: Population-based detection of structural variants from Read-Depth signal

Description

Interactive summary of the individual bins with abnormal coverage as detected by 'call.abnomal.cov'.

Usage

sv.summary.interactive(res.df, height = "500px")

Arguments

res.df	the data.frame with the results.
height	the height of the plot in the webpage. Default is "500px".

Details

A number of simple metrics are displayed, to get an idea of the quality of the calls. For normal samples we would expect: the amount of called genome in each sample to be somewhat similar; the copy number estimates to locate near integer values; No systematic calls (i.e. called in all samples). The different tabs of the application display related metrics. The use can interactively tweak a number of filtering parameter to get a subset of high-quality calls. These filtering parameters are

• False Discovery Ratesignificance threshold, reduce it to get higher confidence calls.

• Deviation from the CN 2how different a call should be compared to the estimated *C*opy *N*umber 2. Force a minimum deviation if you see calls too close to CN 2 (second tab).

• Maximum of single bins (Kb)automatically chooses a significance threshold that gives the specified maximum of genome affected by single-bin calls. Useful to force higher stringency for outlier samples (but keep them).

• Minimum read coverage in referencemappability threshold. Increase this number to remove calls in regions with low coverage in the reference samples.

Value

a shiny app in the web browser. When the 'Export' button is pressed, the resulting data.frame is returned.

Author(s)

Jean Monlong

jmonlong/PopSV documentation built on Sept. 15, 2019, 9:29 p.m.