compare_profiles {seqCAT} | R Documentation

## Binary SNV profile comparisons

### 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)

[Package seqCAT version 1.10.0 Index]