ConsensusFromDataframe: Create Consensus Object from Data Frame

In HatsuneCode/TrustVDJ: Tools for Immune Repertoire Analysis

Create Consensus Object from Data Frame

Description

Create Consensus Object from Data Frame

Usage

ConsensusFromDataframe(
  Df,
  properties = NULL,
  rm_allele = FALSE,
  verbose = TRUE
)

Arguments

Df	data.frame.
properties	list.
rm_allele	logical. remove allele, such as TRA1-1*01 to TRA1-1.
verbose	logical.

Value

an object of consensus

Examples

# file paths
airr_file   = system.file('extdata', '10x_airr_rearrangement.tsv.gz', package = 'TrustVDJ')
contig_file = system.file('extdata', '10x_all_contig_annotations.csv.gz', package = 'TrustVDJ')
# read file
data        = Read10x(airr_file = airr_file, contig_file = contig_file)
# create consensus object
consensus   = ConsensusFromDataframe(data, properties = list(
 ConsenID = 'raw_consensus_id', ClonoID = 'clone_id', Barcode = 'cell_id', 
 Vgene = 'v_call', Dgene = 'd_call', Jgene = 'j_call', Cgene = 'c_call',
 UMIs = 'duplicate_count', Reads = 'consensus_count') )
consensus

HatsuneCode/TrustVDJ documentation built on Aug. 13, 2022, 9:36 p.m.