summary_qc: Quality control of NanoSatellite delineation and segmentation

In arnederoeck/NanoSatelliteR: QC, plotting, and clustering of tandem repeat segmentation created by NanoSatellite.

Description

summary_qc() returns (box)plots and suggested cutoff values to filter tandem repeat segmentations based on normalized distance.

Usage

summary_qc(df)

Arguments

df	data.frame generated by load_summary()

Details

This function requires a data frame as generated by load_summary(). summary_qc() will analyze the normalized "flank" and "center" dynamic time warping distance, respectively corresponding to delineation of tandem repeat squiggles from flanking squiggles, and the segmentation of the tandem repeat squiggle. A scatter plot of both distances is shown as well as boxplots for the individual metrics. In addition, cutoff values corresponding to 1.5 times the interquartile range from the 75th percentile are returned.

Examples

df <- load_summary("/storage/NanoSatellite_chunks/")
qc <- summary_qc(df)

arnederoeck/NanoSatelliteR documentation built on May 6, 2019, 1:35 a.m.