quantContig {scRepertoire} | R Documentation |
This function takes the output from combineTCR(), combineBCR(), or e xpression2List() and quantifies unique clonotypes. The unique clonotypes can be either reported as a raw output or scaled to the total number of clonotypes recovered using the scale parameter. Multiple sequencing runs can be group together using the group parameter. If a matrix output for the data is preferred, set exportTable = TRUE.
quantContig( df, cloneCall = "gene+nt", scale = FALSE, group = NULL, exportTable = FALSE )
df |
The product of combineTCR() combineBCR() or expression2List(). |
cloneCall |
How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt), CDR3 amino acid (aa), or CDR3 gene+nucleotide (gene+nt). |
scale |
Converts the graphs into percentage of unique clonotypes. |
group |
The column header used for grouping. |
exportTable |
Returns the data frame used for forming the graph |
ggplot of the total or relative unique clonotypes
#Making combined contig data x <- contig_list combined <- combineTCR(x, rep(c("PX", "PY", "PZ"), each=2), rep(c("P", "T"), 3), cells ="T-AB") quantContig(combined, cloneCall="gene+nt", scale = TRUE)