clonalRelatedness: Clonal relatedness

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

Description

Calculates the clonal relatedness for each sample in a list of data frames.

Usage

clonalRelatedness(list, editDistance = 10)

Arguments

list	A list data frames of unproductive or productive nucleotide sequences or productive nucleotide sequences. Nucleotide and count are required columns.
editDistance	An integer giving the minimum edit distance that the sequence must be less than or equal to. See details below.

Details

Clonal relatedness is the proportion of nucleotide sequences that are related by a defined edit distance threshold. The value ranges from 0 to 1 where 0 indicates no sequences are related and 1 indicates all sequences are related.

Edit distance is a way of quantifying how dissimilar two sequences are to one another by counting the minimum number of operations required to transform one sequence into the other. For example, an edit distance of 0 means the sequences are identical and an edit distance of 1 indicates that the sequences different by a single amino acid or nucleotide.

Value

Returns a data frame with the calculated clonal relatedness for each sample.

Examples

file.path <- system.file("extdata", "IGH_sequencing", package = "LymphoSeq")

file.list <- readImmunoSeq(path = file.path)

clonal.relatedness <- clonalRelatedness(list = file.list, editDistance = 10)

# Merge results with clonality table
clonality <- clonality(file.list = file.list)
merged <- merge(clonality, clonal.relatedness)

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.