getFilename: downloads files from aws storage and returns local filepath

In cpanse/tartare: Raw ground spectra recorded on Thermo Fisher Scientific mass spectrometers

Description

calls the query method of an ExperimentHub object query and returns the local filenames. Of note: for proprietary reasons, a file.link is set to the cached files. It seems that the New RawfileReader .Net library is only accepting files ending with raw. The overall file size is 285MB.

Usage

getFilename(eh, query = c("tartare"))

Arguments

eh	ExperimentHub object.
query	a query string, e.g., c('tartar', '20190710_003_PierceHeLaProteinDigestStd.raw')

Value

returns file(s) contained in the tartare package.

Author(s)

Christian Panse <[e-mail]>, 2019-10

See Also

• browseVignettes('tartare')

• query

Examples

library(ExperimentHub)
eh <- ExperimentHub()
query(eh, c('tartare'))

## Not run: 
(files <- getFilename(eh))
library(MsBackendRawFileReader)

be <- lapply(files, function(f){
if (grepl("mzXML$", f))
    backendInitialize(MsBackendMzR(), files = f)
else
    backendInitialize(MsBackendRawFileReader(), files = f, extra=FALSE)
})

## End(Not run)

## Not run: 
hfx.filename <- .query(eh, c('tartar', '20190710_003_PierceHeLaProteinDigestStd.raw'))
x <- .cnew ("Rawfile", hfx.filename)
x$GetInfoValues()

## End(Not run)

cpanse/tartare documentation built on Nov. 4, 2019, 9:14 a.m.