percentKmer: Examining the relative composition of kmer motifs in clones.

In ncborcherding/scRepertoire: A toolkit for single-cell immune receptor profiling

Examining the relative composition of kmer motifs in clones.

Description

This function the of kmer for nucleotide (nt) or amino acid (aa) sequences. Select the length of the kmer to quantify using the motif.length parameter.

Usage

percentKmer(
  input.data,
  chain = "TRB",
  cloneCall = "aa",
  group.by = NULL,
  order.by = NULL,
  motif.length = 3,
  top.motifs = 30,
  exportTable = FALSE,
  palette = "inferno"
)

Arguments

input.data	The product of combineTCR(), combineBCR(), or combineExpression()
chain	"TRA", "TRB", "TRG", "TRG", "IGH", "IGL"
cloneCall	How to call the clone - CDR3 nucleotide (nt) or CDR3 amino acid (aa)
group.by	The variable to use for grouping
order.by	A vector of specific plotting order or "alphanumeric" to plot groups in order
motif.length	The length of the kmer to analyze
top.motifs	Return the n most variable motifs as a function of median absolute deviation
exportTable	Returns the data frame used for forming the graph.
palette	Colors to use in visualization - input any hcl.pals

Value

ggplot of percentage of kmers as a heatmap

Examples

#Making combined contig data
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))
percentKmer(combined, 
            chain = "TRB", 
            motif.length = 3)

ncborcherding/scRepertoire documentation built on Nov. 5, 2024, 2:05 p.m.