rabhit (version 0.2.5)

deletionsByVpooled: Single chromosomal D or J gene deletions inferred by the V pooled method

Description

The deletionsByVpooled function inferes single chromosomal deletion for D and J gene .

Usage

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()
)

Value

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.

Arguments

clip_db

a data.frame in AIRR format. See details.

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 data.frame created by deletionsByBinom.

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 list created by nonReliableVGenes.

Details

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)

Examples

# \donttest{
data(samples_db)

# Infering V pooled deletions
del_db <- deletionsByVpooled(samples_db)
head(del_db)
# }