Description Usage Arguments Details Value Author(s) See Also Examples
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
.
1 2 3 4 5 6 |
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) |
... |
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.
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) |
Julia Bischof
clones.CDR3Length
, plotClonesCDR3Length
, plotClonesCopyNumber
, geneUsage
1 2 3 4 5 6 | ## 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)
|
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