getdata2 {enviGCMS} | R Documentation |
Get XCMSnExp object in one step from structured folder path for xcms 3.
Description
Get XCMSnExp object in one step from structured folder path for xcms 3.
Usage
getdata2(
path,
index = FALSE,
snames = NULL,
sclass = NULL,
phenoData = NULL,
BPPARAM = BiocParallel::SnowParam(),
mode = "onDisk",
ppp = xcms::CentWaveParam(ppm = 5, peakwidth = c(5, 25), prefilter = c(3, 5000)),
rtp = xcms::ObiwarpParam(binSize = 1),
gpp = xcms::PeakDensityParam(sampleGroups = 1, minFraction = 0.67, bw = 2, binSize =
0.025),
fpp = xcms::FillChromPeaksParam()
)
Arguments
path |
the path to your data |
index |
the index of the files |
snames |
sample names. By default the file name without extension is used |
sclass |
sample classes. |
phenoData |
data.frame or NAnnotatedDataFrame defining the sample names and classes and other sample related properties. If not provided, the argument sclass or the subdirectories in which the samples are stored will be used to specify sample grouping. |
BPPARAM |
used for BiocParallel package |
mode |
'inMemory' or 'onDisk' see ‘?MSnbase::readMSData' for details, default ’onDisk' |
ppp |
parameters for peaks picking, e.g. xcms::CentWaveParam() |
rtp |
parameters for retention time correction, e.g. xcms::ObiwarpParam() |
gpp |
parameters for peaks grouping, e.g. xcms::PeakDensityParam() |
fpp |
parameters for peaks filling, e.g. xcms::FillChromPeaksParam(), PeakGroupsParam() |
Details
This is a wrap function for metabolomics data process for xcms 3.
Value
a XCMSnExp object with processed data