geneUsage | R Documentation |
The geneUsage
function calculates the relative gene usage.
geneUsage( clip_db, chain = c("IGH", "IGK", "IGL", "TRB"), genes_order = NULL, rmPseudo = TRUE )
clip_db |
a |
chain |
the IG/TR chain: IGH,IGK,IGL,TRB. Default is IGH. |
genes_order |
A vector of the genes by the desired order. Default is by GENE.loc |
rmPseudo |
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)
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
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