Package 'MsExperimentStash'

Stash for MsExperimentFiles

Description

The MsExperiment::MsExperimentFiles class stores files (or rather file names) that are part of a mass spectrometry experiment.

The supported stash formats for MsExperimentFiles objects are listed in the sections below.

Usage

## S4 method for signature 'MsExperimentFiles,PlainTextParam'
saveMsObject(object, param, ...)

## S4 method for signature 'MsExperimentFiles,PlainTextParam'
readMsObject(object, param, ...)

## S4 method for signature 'MsExperimentFiles'
saveObject(x, path, ...)

## S4 method for signature 'MsExperimentFiles,AlabasterParam'
saveMsObject(object, param, ...)

## S4 method for signature 'MsExperimentFiles,AlabasterParam'
readMsObject(object, param, ...)

Arguments

object	An MsExperimentFiles object.
param	An MsStash::AlabasterParam or MsStash::PlainTextParam.
...	Currently ignored.
x	An MsExperimentFiles object.
path	For saveObject(): character(1) with the path where the object should be stored into.

Value

readMsObject() returns a MsExperiment::MsExperimentFiles object.

Text-file format, PlainTextParam

The text-file format stash folder for MsExperimentFile objects contains a file ms_experiment_files.txt with two tabulator separated columns name and files. Each row (except the first) is one element of the MsExperimentFile, the first defining the object's names and the second its content, which represents a characted vector with the file name(s), separated by a "|" (if more than one).

alabaster-based format, AlabasterParam

The MsExperimentFiles stash folder contains the alabaster-specific OBJECT file and a sub-folder x with the MsExperimentFiles content serialized by alabaster.base.

Author(s)

Johannes Rainer

Examples

library(MsExperiment)

fls <- MsExperimentFiles(list(input = c("file.mzML", "file2.mgf")))

## Define the path to the stash
d <- file.path(tempdir(), "ms_file_stash")

## Stash the object in alabaster format
saveMsObject(fls, AlabasterParam(d))

## The content of the stash: subfolder x contains the *character list*
## saved through the *alabaster.base* package.
library(fs)
dir_tree(d)

## Restore the object from stash
res <- readMsObject(MsExperimentFiles(), AlabasterParam(d))
res

## In addition, it is possible to read the object also with the
## *alabaster.base* functionality
library(alabaster.base)
res <- readObject(d)

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