compare_profiles: Binary SNV profile comparisons

In seqCAT: High Throughput Sequencing Cell Authentication Toolkit

Description

Overlap and compare genotypes in two SNV profiles.

Usage

compare_profiles(profile_1, profile_2, mode = "intersection")

Arguments

profile_1	The first SNV profile (GRanges object).
profile_2	The second SNV profile (GRanges object).
mode	Merge profiles using "union" or "intersection" (character).

Details

This is a function for finding overlapping variants in two different SNV profiles (stored as GenomicRanges objects), followed by comparing the genotypes of the overlapping variants. The "compare_overlaps" function calls the "add_metadata" function twice in succession in order to merge the metadata for the two profiles (supplied as GRanges objects), returns the results as a dataframe, compares the genotypes of the overlapping variants using the "compare_genotypes" function and, finally, returns the final dataframe with all variant overlaps and their similarity.

Value

A dataframe.

Examples

# Load test data
data(test_profile_1)
data(test_profile_2)

# Compare the two profiles
comparison <- compare_profiles(test_profile_1, test_profile_2)

seqCAT documentation built on Nov. 8, 2020, 7:36 p.m.