manta_isec_stats: Manta Comparison Metrics

In pdiakumis/woofr: Helper R Functions for woof

Manta Comparison Metrics

Description

Returns evaluation metrics from comparing two Manta call sets.

Usage

manta_isec_stats(mi, samplename, flab)

Arguments

mi	Output from manta_isec.
samplename	Sample name (used for labelling).
flab	File name (used for labelling).

Value

A single row tibble with the following columns:

• sample: samplename

• flabel: flab

• run1_count: total variants in first file

• run2_count: total variants in second file

• TP: in first and second

• FP: in first but not second

• FN: in second but not first

• Recall: TP / (TP + FN)

• Precision: TP / (TP + FP)

• Truth: TP + FN

Examples

## Not run: 
f1 <- "path/to/run1/manta.vcf.gz"
f2 <- "path/to/run2/manta.vcf.gz"
mi <- manta_isec(f1, f2, "sampleA", "manta1")
manta_isec_stats(mi, "sampleA", "manta1")

## End(Not run)

pdiakumis/woofr documentation built on Jan. 4, 2024, 11:22 a.m.