bcRep (version 1.3.2)

clones.CDR3Length: CDR3 length distribution of clones

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)

...

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)

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.

See Also

clones.CDR3Length, plotClonesCDR3Length, plotClonesCopyNumber, geneUsage

Examples

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)