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

Description Usage Arguments Details Value Examples

View source: R/functions.R

Description

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

Usage

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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()
)

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. Defualt 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:

Value

A data.frame, in which each row is the single chomosome deletion inference of a gene.

The output containes the following columns:

Examples

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data(samples_db)

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

rabhit documentation built on July 12, 2020, 1:06 a.m.