| analyzeTable {Mosaic} | R Documentation |
Run a series of analyses on a feature table data.frame
analyzeTable(df = tab1$df, intensities = tab1$intensities,
groups = tab1$anagroupnames, analyze = c("Basic analysis",
"clara_cluster", "p-values", "Peak shapes", "PCA features", "PCA samples"),
normalize = T, useNormalized = T, MSData = NULL, ppm = 5,
controlGroup = NULL, numClusters = 2)
df |
a data.frame with numeric (intensity) values, rt and mz values |
intensities |
the intensity column names, before normalization (without __norm suffix), will be automatically renamed if useNormalized. |
groups |
named list of non-normalized intensity columns listed by group (as supplied by $anagroupnames of MosaicFT objects), will be automatically renamed if useNormalized. |
analyze |
character vector to select the analyses to be run: "Basic analysis", "clara_cluster", "p-values", "Peak shapes" |
normalize |
normalze intensity columns |
MSData |
a (named) list of xcmsRaw objects, e.g. generated by Mosaic::loadRawM, OR an MSnbase OnDiskMSnExp object required for peak shape analysis |
ppm |
ppm range for peak shape analysis |
controlGroup |
control group for foldChange (part of Basic analysis) analysis (optional) |
numClusters |
number of clusters for clara_clusters analysis |
useNormalize |
use normalized values for analyses; will trigger normalize if there is no normalized data available for all selected intensity columns |