ref_cluster_sizes: Cluster size probabilities in naive reference repertoire

In HetzDra/turboGliph: Find Specificity Groups with GLIPH and GLIPH2 Method

Cluster size probabilities in naive reference repertoire

Description

"ref_cluster_sizes" is a list containing two matrices with probabilities for cluster sizes in a naive reference repertoire. The element named "original" contains the probabilities used in the original GLIPH algorithm. Here, the same probabilities are used for all sample sizes. The element names "simulated" contains probabilities determined by us. Since the distribution of cluster sizes depend on the sample size, we estimated with GLIPH the probabilities for different sample sizes in a 500-step simulation using different numbers of random sequences from the reference database (125, 250, 500, 1000, 2000, 4000, 6000, 8000, 10000). For scoring, the probabilities from the dataset corresponding the closest to the sample size are used.

Usage

data(ref_cluster_sizes)

Format

An object of class list of length 2.

Source

Glanville, Jacob, et al. "Identifying specificity groups in the T cell receptor repertoire." Nature 547.7661 (2017): 94.

HetzDra/turboGliph documentation built on Oct. 2, 2022, 2:22 a.m.