VDJ_variants_per_clone: Wrapper for variant analysis by clone

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Wrapper for variant analysis by clone

Description

Returns statistics and plots to examine diversity of any sequence or metadata item within clones on a by sample level or global level

Usage

VDJ_variants_per_clone(
  VDJ,
  variants.of,
  clonotypes.col,
  stringDist.method,
  split.by,
  platypus.version
)

Arguments

VDJ	VDJ output of the VDJ_GEX_matrix (VDJ_GEX_matrix.output[[1]]). VDJ matrix supplemented with with MIXCR information is also valid
variants.of	Character vector. Defaults to c("VDJ_cdr3s_aa", "VJ_cdr3s_aa"). Column name(s) of VDJ to examine variants of. If more than one name is given, these columns will be pasted together. The default will therefore return statistics on the number of variants of VDJ and VJ cdr3s in every clone
clonotypes.col	Column name of the VDJ column containing clonotype information. Defaults to "clonotype_id_10x". This is useful if alternative clonotyping strategies have been used and are stored in other columns
stringDist.method	Character. Passed to Biostrings::strinDist. Method to calculate distance between variants of a clone. Defaults to "levenshtein". Other options are "hamming", "quality". If "hamming" variants of a clone will be shortened from the end to the shortest variant to make all input sequences the same length.
split.by	Character. Defaults to "sample_id". Column name of VDJ to split the analysis by. This is necessary, if clonotyping was done on a per sample level (e.g. "clonotype1" in sample 1 is not the same sequence as "clonotype1" in sample 2). If clonotyping was done across samples and no splitting is necessary input "none"
platypus.version	Character. Only "v3" available.

Value

Returns a list of dataframes. Each dataframe contains the statistics of one split.by element (by default: one sample)

Examples

variants_per_clone <- VDJ_variants_per_clone(VDJ = Platypus::small_vgm[[1]]
,variants.of = c("VDJ_cdr3s_aa", "VJ_cdr3s_aa"),
stringDist.method = "levenshtein", split.by = "sample_id")

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.