clones.CDR3Length: CDR3 length distribution of clones

In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description

This function gives information about the CDR3 length distribution of clones. Results can be returned as relative or absolute values and be visualized as a barplot, using plotClonesCDR3Length.

Usage

clones.CDR3Length(CDR3Length = NULL, functionality = NULL, junctionFr = NULL, 
     abundance=c("relative","absolute"), ...)
     
plotClonesCDR3Length(CDR3Length=NULL,functionality=NULL, junctionFr=NULL,   
     color=c("orange","darkblue","gray"), abundance=c("relative","absolute"), 
     title=NULL, PDF=NULL,...)

Arguments

CDR3Length	Vector of CDR3 length of clones (amino acids or nucleotides)
functionality	Vector of functionality of clones (same order than CDR3Length)
junctionFr	Vector of junction frame usage of clones (same order than CDR3Length)
abundance	Shall relative or absolute values be returned? (default: relative)
color	color used for plots (default: c("orange","darkblue","gray"))
title	title of the plot (optional)
PDF	PDF project name (see Details)
...

Details

The PDF character string should be only the project name (without ".pdf"). For simple analysis of the CDR3 length, a plot called "PDF"_CDR3-length.pdf will be saved to the working direktory.

If CDR3Length.Func = T a figure containing CDR3 length vs. functionality is saved (called "PDF"_CDR3-length_vs_Functionality.pdf) and if CDR3Length.JunctionFr = T a figure containing CDR3 length vs. junction fram usage (called "PDF"_CDR3-length_vs_Junction-frame.pdf) is saved.

Value

Output is a list containing

CDR3_length	relative or absolute abundances of CDR3 length
CDR3_length_vs_functionality	(optional)
CDR3_length_vs_junction_frame	(optional)

Author(s)

Julia Bischof

See Also

clones.CDR3Length, plotClonesCDR3Length, plotClonesCopyNumber, geneUsage

Examples

## Not run: data(clones.ind)
clones.CDR3Length(CDR3Length = clones.ind$CDR3_length_AA, 
     functionality = clones.ind$Functionality_all_sequences)
plotClonesCDR3Length(CDR3Length = clones.ind$CDR3_length_AA, 
     functionality = clones.ind$Functionality_all_sequences)
## End(Not run)

bcRep documentation built on May 2, 2019, 5:14 a.m.