compare_many {seqCAT} | R Documentation

## Comparisons of many SNV profiles

### Description

Overlap and compare genotypes in many SNV profiles.

### Usage

    compare_many(many, one = NULL, a = 1, b = 5)

### Arguments

`many` | SNV profiles to be compared (list of GRanges objects).
`one` | SNV profile to be compared to all others (GRanges object).
`a` | Similarity score parameter a (integer).
`b` | Similarity score parameter b (integer).

### Details

This is a function that compares all the combinations of the SNV profiles input to it, either in a one-to-many or many-to-many manner. It returns both a dataframe containing summary statistics for all unique combinations and a list of dataframes with all the performed comparisons, for easy re-use and downstream analyses of said comparisons.

### Value

A list of summary statistics and comparisons.

### Examples

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

    # Perform many-to-many comparisons
    profiles <- list(test_profile_1, test_profile_2)
    comparisons <- compare_many(profiles)

    # View aggregate similarities
    ## Not run: comparisons[[1]])

    # View data of first comparison
    ## Not run: head(comparisons[[2]][[1]])

[Package seqCAT version 1.2.1 Index]