Description Usage Arguments Value See Also Examples
This function allows to examine specificity of enzymatic digestion (or chemical cleavage), based on MS/MS identification result (search without any enzyme specification, or "unspecific" search). Can be useful to check cleavage selectivity & efficiency of each enzyme used in multiple digestion or of less-specific enzymes.
1 | plotCleavage(seq, after, hide.plot = FALSE, normalize = FALSE)
|
seq |
A character vector of identified peptide sequences without any modifications. Should only made up of 20 amino acids one letter characters. |
after |
A character vector of peptide sequences after cleavage site. Only the first amino acid is used, but can be of longer length. |
hide.plot |
Logical, default FALSE. If set to TRUE, no plot will be drawn. Can be used just to obtain a data.frame of cleavage site frequency for manual plotting. |
normalize |
Logical, default FALSE (stacked barchart of cleaved and not-cleaved). |
If (and only if) assigned to a variable, this function returns a data.frame with columns (AA
, Freq
, terminal
, cleavage
) for custom plotting.
1 2 3 | data(Elastase)
plotCleavage(Elastase$Sequence, Elastase$AAs.After)
plotCleavage(Elastase$Sequence, Elastase$AAs.After, normalize=TRUE)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.