Ig_SE: IGHV gene family usage in vaccine-challenged B-cell...

In snaketron/test_repo: Differential gene usage in immune repertoires

Description

A small example database subset from study evaluating vaccine-induced changes in B-cell populations publicly provided by R-package alakazam (version 0.2.11). It contains IGHV gene family usage, reported in four B-cell populations (samples IgM, IgD, IgG and IgA) across two timepoints (conditions = -1 hour and +7 days).

Usage

data("Ig_SE")

Format

A SummarizedExperiment object with 1) assay data (rows = gene name, columns = repertoires) and 2) column data.frame in which the sample names and the corresponding biological condition labels are noted.

Source

R package: alakazam version 0.2.11

References

Laserson U and Vigneault F, et al. High-resolution antibody dynamics of vaccine-induced immune responses. Proc Natl Acad Sci USA. 2014 111:4928-33.

Examples

# inspect the data
data(Ig_SE)

# repertoire information: must have the two columns: 'condition', 'sample_id'
SummarizedExperiment::colData(Ig_SE)

# assay counts (gene frequency usage)
SummarizedExperiment::assay(x = Ig_SE)

snaketron/test_repo documentation built on Dec. 23, 2021, 3:28 a.m.