scoringMatrix: Bhattacharyya, Similarity, Sorensen, or PSI matrix

In shashidhar22/LymphoSeq2: Analyze high-throughput sequencing of T and B cell receptors

Bhattacharyya, Similarity, Sorensen, or PSI matrix

Description

Calculates the Bhattacharyya coefficient, Similarity score, Sorensen Index, or Percent Similarity Index of all pairwise comparison from a list of data frames.

Usage

scoringMatrix(productive_table, mode = "Bhattacharyya")

Arguments

productive_table	A tibble of productive sequences generated by the LymphoSeq function productiveSeq(). "duplicate_frequency" and "junction_aa" are a required columns.
mode	The mode to use for calculating pairwise similarity. Can take the values "Bhattacharyya", "Similarity", "Sorensen", or "PSI". Default is "Bhattacharyya".

Value

A data frame of Bhattacharyya coefficients, Similarity scores, Sorensen Index, or Percent Similarity Index calculated from all pairwise comparisons from a list of repertoire_id data frames. Both metrics measure the amount of overlap between two samples. The value ranges from 0 to 1 where 1 indicates the sequence frequencies are identical in the two samples and 0 indicates no shared frequencies.

See Also

pairwisePlot() for plotting results as a heat map.

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
 package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(path = file_path, threads = 1)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)
amino_table <- LymphoSeq2::productiveSeq(study_table,
 aggregate = "junction_aa")
bhattacharyya_matrix <- LymphoSeq2::scoringMatrix(
  productive_table = amino_table,
  mode = "Bhattacharyya"
)
similarity_matrix <- LymphoSeq2::scoringMatrix(
  productive_table = amino_table,
  mode = "Similarity"
)
sorensen_matrix <- LymphoSeq2::scoringMatrix(
  productive_table = amino_table,
  mode = "Sorensen"
)
psi_matrix <- LymphoSeq2::scoringMatrix(
  productive_table = amino_table,
  mode = "PSI"
)

shashidhar22/LymphoSeq2 documentation built on Jan. 16, 2024, 4:29 a.m.