Ig_SE {IgGeneUsage} | R Documentation |
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).
data("Ig_SE")
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.
R package: alakazam version 0.2.11
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.
# 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)