The geneUsage function calculates the relative gene usage.
geneUsage(
clip_db,
chain = c("IGH", "IGK", "IGL", "TRB"),
genes_order = NULL,
rmPseudo = TRUE
)A data.frame, in which each row is the relative gene usage value per individual.
The output containes the following columns:
subject: the subject name.
gene: the gene call
frac: the relative gene usage of the gene
a data.frame in AIRR format. See details.
the IG/TR chain: IGH,IGK,IGL,TRB. Default is IGH.
A vector of the genes by the desired order. Default is by GENE.loc
if TRUE non-functional and pseudo genes are removed. Default is TRUE.
The function accepts a data.frame in AIRR format (https://changeo.readthedocs.io/en/stable/standard.html) containing the following columns:
'subject': The subject name
'v_call': V allele call(s) (in an IMGT format)
'd_call': D allele call(s) (in an IMGT format, only for heavy chains)
'j_call': J allele call(s) (in an IMGT format)