compare_many: Comparisons of many SNV profiles

Description Usage Arguments Details Value Examples

View source: R/compare_many.R

Description

Overlap and compare genotypes in many SNV profiles.

Usage

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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

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# 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]])

seqCAT documentation built on Nov. 1, 2018, 2:07 a.m.