deletionsByBinom | R Documentation |
The deletionsByBinom
function inferes double chromosome deletion events by relative gene usage.
deletionsByBinom( clip_db, chain = c("IGH", "IGK", "IGL"), nonReliable_Vgenes = c(), genes_order = NULL )
clip_db |
a |
chain |
the IG/TR chain: IGH,IGK,IGL,TRB. Default is IGH. |
nonReliable_Vgenes |
a list of known non reliable gene assignments. A |
genes_order |
A vector of the genes by the desired order. Default is by GENE.loc |
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 double chomosome deletion inference of a gene.
The output containes the following columns:
subject
: the subject name.
gene
: the gene call
frac
: the relative gene usage of the gene
cutoff
: the the cutoff of for the binomial test
pval
: the p-value of the binomial test
deletion
: if a double chromosome deletion event of a gene occured.
# Load example data and germlines data(samples_db) # Selecting a single individual clip_db = samples_db[samples_db$subject=='I5', ] # Infering haplotype del_binom_df = deletionsByBinom(clip_db) head(del_binom_df)
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