Package 'MsBackendRawFileReader'

RawFileReader_read_peaks benchmark

Description

derives numbers to evaluate time performance for reading a single spectrum in dependency from the chunk size (how many spectra are read in one function call) for reading different numbers of overall spectra.

Usage

ioBenchmark(
  nv = c(1000, 5000, 10000),
  sizev = c(8, 16, 32, 64, 128, 256, 8, 16, 32, 64, 128, 256, 8, 16, 32, 64, 128, 256, 8,
    16, 32, 64, 128, 256, 8, 16, 32, 64, 128, 256, 8, 16, 32, 64, 128, 256),
  rawfile
)

Arguments

nv	number of spectra to be read.
sizev	number of spectra write and parsed in one single junk.
rawfile	the Thermo Fisher Scientific raw file.

Value

data.frame

Examples

eh <- ExperimentHub::ExperimentHub()
EH4547  <- normalizePath(eh[["EH4547"]])
(rawfileEH4547  <- paste0(EH4547 , ".raw"))
if (!file.exists(rawfileEH4547 )){
  file.link(EH4547 , rawfileEH4547)
  }
S <- ioBenchmark(1000, c(128, 256, 128, 256), rawfile=rawfileEH4547)

---

MsBackendRawFileReader

Description

MsBackendRawFileReader

Usage

MsBackendRawFileReader()

## S4 method for signature 'MsBackendRawFileReader'
filterScan(object, filter = character(), ...)

## S4 method for signature 'MsBackendRawFileReader'
scanType(object, ...)

## S4 method for signature 'MsBackendRawFileReader'
scanIndex(object, ...)

Arguments

object	MsBackendRawFileReader object
filter	filter string
...	Arguments to be passed to methods.

Value

a MsBackendRawFileReader object.

a character vector of scan types.

a character vector of scan index.

Examples

beRaw <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(),
  files = rawrr::sampleFilePath())
beRaw |> MsBackendRawFileReader::filterScan('Ms')
beRaw <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(),
  files = rawrr::sampleFilePath())
scanType(beRaw) |> head()
beRaw <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(),
  files = rawrr::sampleFilePath())
scanIndex(beRaw) |> head()

---

RawFileReader-based backend

Description

The 'MsBackendRawFileReader' inherits all slots and methods from the base 'MsBackendDataFrame' (in-memory) backend. It overrides the base 'mz' and 'intensity' methods as well as 'peaksData' to read the respective data from the original raw data files.

The validator function has to ensure that the files exist and that required column names are present.

The 'backendInitialize' method reads the header data from the raw files and hence fills the 'spectraData' slot.

Author(s)

Christian Panse (2019-2021)

Examples

beRaw <- Spectra::backendInitialize(MsBackendRawFileReader::MsBackendRawFileReader(),
  files = rawrr::sampleFilePath())
beRaw
Spectra::msLevel(beRaw)

---