deletionsByVpooled | R Documentation |
The deletionsByVpooled
function inferes single chromosomal deletion for D and J gene .
deletionsByVpooled( clip_db, chain = c("IGH", "IGK", "IGL"), deletion_col = c("d_call", "j_call"), count_thresh = 50, deleted_genes = "", min_minor_fraction = 0.3, kThreshDel = 3, nonReliable_Vgenes = c() )
clip_db |
a |
chain |
the IG chain: IGH,IGK,IGL. Default is IGH. |
deletion_col |
a vector of column names for which single chromosome deletions should be inferred. Default is j_call and d_call. |
count_thresh |
integer, the minimun number of sequences mapped to a specific V gene to be included in the V pooled inference. |
deleted_genes |
double chromosome deletion summary table. A |
min_minor_fraction |
the minimum minor allele fraction to be used as an anchor gene. Default is 0.3 |
kThreshDel |
the minimum lK (log10 of the Bayes factor) to call a deletion. Default is 3. |
nonReliable_Vgenes |
a list of known non reliable gene assignments. A |
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 single chomosome deletion inference of a gene.
The output containes the following columns:
subject
: the subject name.
gene
: the gene call
deletion
: chromosome deletions inferred. Encoded 1 for deletion and 0 for no deletion.
k
: the Bayesian factor value for the deletion inference.
counts
: the appereance count of the gene on each chromosome, the counts are seperated by a comma.
data(samples_db) # Infering V pooled deletions del_db <- deletionsByVpooled(samples_db) head(del_db)
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