clonality: Annotate clonality

In victoraLab/clonality: Easily Define Groups Of T/B Cells

Annotate clonality

Description

The clonality package returns the input table with the clonality annotations.

Usage

clonality(
  data = "example.xlsx",
  output = "output",
  ident_col = "Sequence_ID",
  vgene_col = "V_GENE_and_allele",
  jgene_col = "J_GENE_and_allele",
  cdr3_col = "JUNCTION",
  cell = "T",
  output_original = FALSE,
  mismatch = 0,
  suffix = NULL,
  search_genename = TRUE,
  stringdist_method = "osa"
)

Arguments

data	A data frame object or the full path to a xlsx with repertoire data.
output	Character. The output name. Default: output.
ident_col	Character. The column with unique sequence IDs. Default: Sequence_ID.
vgene_col	Character. The column with V gene names. Default: V_GENE_and_allele.
jgene_col	Character. The column with J gene names. Default: J_GENE_and_allele.
cdr3_col	Character. The column with CDR3 sequences - nt/aa. Default: JUNCTION.
cell	Character. Choose T for T cell or B for B cell. Default: T.
output_original	Logical. ifTRUE, output and input have same format. Default: FALSE.
mismatch	Numeric. Percent of mismatches allowed in subgroups. 0 == most_stringent, 1 == less_stringent. Default: 0
suffix	Character. String to be appended to the clonality ID.
search_genename	Logical. Accepts IMGT nomenclature and simplify gene IDs. Default: TRUE.
stringdist_method	Character. Method for distance calculation. See ?stringdist-metrics for more methods.

Examples

clonality(data = tra)
clonality(data = trb)
clonality(data = 'example.xlsx')

victoraLab/clonality documentation built on March 19, 2024, 7:41 p.m.