as.matrix.MSMSpepXML: Transforms an 'MSMSpepXML' object in a simplified matrix.
In lgatto/RpepXML: R interface to the pepXML standard

Description Usage Arguments Value Warning Author(s) Examples

This function transforms an "MSMSpepXML" instance in a matrix. The object is significantly simplified, as only the first search results and hits are kept. The matrix includes query index, spectrum id, ion score, peptide sequence, the number of proteins inferred and the protein(s) name(s).

1	as.matrix.MSMSpepXML(x, ..., all = TRUE)

`x`	an object of class `"MSMSpepXML"`.
`...`	further options passed to next methods.
`all`	logical, whether all rows or only the ones with identified peptides should ne returned.

A matrix.

If search results and hits are removed, warnings are issued.

Laurent Gatto

 pepxml <- system.file("extdata","tinySearch.pepXML",package="RpepXML")
 x <- parseMSMSpepXML(pepxml)
 as.matrix(x)
 as.matrix(filterHits(x),all=TRUE)
 as.matrix(filterHits(x),all=FALSE)