lgatto/MSnbase — pull request #24 by sgibb (2014-03-24 14:35:09+00:00)
Title: add idSummary

Dear Laurent,

this PR introduces `idSummary`:
```s
quantFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
full.name = TRUE, pattern = "mzXML$")
identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
full.name = TRUE, pattern = "mzid$")
msexp <- readMSData(quantFile, verbose = FALSE)
msexp <- addIdentificationData(msexp, filenames = identFile,
verbose = FALSE)
idSummary(msexp)
# file identFile coverage
# 1 1 2 0.6
msexp <- removeNoId(msexp)
idSummary(msexp)
# file identFile coverage
# 1 1 2 1
```
I also add a small entry in the vignette (for `removeNoId`, too).

Best wishes,

Sebastian

P.S.: Sorry for the large differences in the files because of the removal of spaces at the line endings.