iterativeSummary: Uncount, sample and iteratively calculate repertoire summary...

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

Uncount, sample and iteratively calculate repertoire summary statistics

Description

Uncount, sample and iteratively calculate repertoire summary statistics

Usage

iterativeSummary(study_table, iterations, min_count = 1000)

Arguments

study_table	A tibble consisting of antigen receptor sequencing imported by the LymphoSeq2 function readImmunoSeq(). "junction_aa", "duplicate_count", and "duplicate_frequency" are required columns. Note that clonality is usually calculated from productive junction sequences. Therefore, it is not recommended to run this function using a productive sequence list aggregated by amino acids.
iterations	Number of iterations to run the sampled clonality metrics.
min_count	The minimum depth to which each repertoire in the study must be sampled to. Default 1000 (the default)

Value

Tibble summarizing the sequence information for each repertoire_id normalized by depth of sequencing

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