Description Usage Arguments Value See Also Examples
This function allows to examine specificity of enzymatic digestion (or chemical cleavage) at dipeptide sequence level, 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 2 | plotCleavageMatrix(seq, after, hide.plot = FALSE, normalize = FALSE,
col.regions = NULL)
|
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). |
col.regions |
Color palette function like |
If assigned to a variable, this function returns a cleavage site matrix, with its row being the first amino acid and its column being the second amino acid.
1 2 |
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