combineBCR: Combining the list of B Cell Receptor contigs
In scRepertoire: A toolkit for single-cell immune receptor profiling

Description Usage Arguments Value See Also Examples

This function consolidates a list of BCR sequencing results to the level of the individual cell barcodes. Using the samples and ID parameters, the function will add the strings as prefixes to prevent issues with repeated barcodes. The resulting new barcodes will need to match the seurat or SCE object in order to use,

combineBCR(
  df,
  samples = NULL,
  ID = NULL,
  removeNA = FALSE,
  removeMulti = FALSE
)

`df`	List of filtered contig annotations from 10x Genomics.
`samples`	The labels of samples.
`ID`	The additional sample labeling option.
`removeNA`	This will remove any chain without values.
`removeMulti`	This will remove barcodes with greater than 2 chains.

List of clonotypes for individual cell barcodes

combineExpression. Unlike combineTCR(), combineBCR produces a column CTstrict of an index of nucleotide sequence and the corresponding v-gene. This index automatically caluclates the Hammings distance between sequences of the same length and will index sequences with > 0.85 normalized Hammings distance with the same ID. If nucleotide sequences meet the threshold, ":HD" will be added to the CTstrict column string.

#Data derived from the 10x Genomics intratumoral NSCLC B cells
BCR <- read.csv("https://ncborcherding.github.io/vignettes/b_contigs.csv", 
stringsAsFactors = FALSE)
combined <- combineBCR(BCR, samples = "Patient1", ID = "Time1")