tenx: Annotate 10x clones

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

Annotate 10x clones

Description

Returns the input with clonality annotation column with clonal definitions.

Usage

tenx(
  data = NULL,
  method = "unique_paired",
  only_productive = T,
  only_true_cells = T,
  clonality_input = NULL,
  cell = "T",
  col_res = c("full"),
  save_files = F,
  add_columns = NULL
)

Arguments

data	Character. Data frame object or the full path to a filtered_contig_annotations.csv file.
method	Character. One of: unique_paired, unique_all, sticky_ends. Default: unique_paired.
only_productive	Logical. Filter non productive chains.
only_true_cells	Logical. Filter low quality / non true cells. Using the default TRUE with the all_contig_annotations.csv file is equivalent of just running on the filtered_contig_annotations.csv.
clonality_input	Named vector. Input parameters for the clonality function.
cell	Character. Possible values: B Bcells, T Tcells, Tgd Gamma Delta T cells.
col_res	Character. Possible values: full paired and unique chain columns, reduced only paired chain columns.
save_files	Logical. Whether to save the Cl matrices as xlsx files or not.
add_columns	Character. Vector containing columns to add into the final result.

Examples

tenx(data = "filtered_contig_annotations", method = "sticky_ends", only_productive = T, clonality_input = c("mismatch" = 0.25), cell = "T",  save.files = F)

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