Constructor function for the rawLayout S3 class, holding information on MSdata grouping and layout options in Metaboseek.
constructRawLayout(rawgrouptable, stem = NULL, msnExp = NULL)
a data.frame with columns File and Group , holding file paths and group names, respectively.
if the file paths in rawgrouptable are not full (e.g. subdirectories of the working directory), this should be the path of the working directory.
if not NULL, must be an
msnExp is provided, will generate an element called
MSnExp_summary in the resulting
rawLayout which is a data.frame
containing information that can be used for normalization. Columns in
sampleNamesFile names of raw files
bpmeans mean values of the basepeak intensity for each file
ticmeans mean values of the TIC intensity for each file
normfactor_bp normalization factor for each file based on base peak
normfactor_tic normalization factor for each file based on TIC intensity peak
Multiplying all intensity values for each file with their normfactors will yield the same mean intensity for all files.
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