summarizeMolecularProfiles {PharmacoGx} | R Documentation |
Given a PharmacoSet with molecular data, this function will summarize the data into one profile per cell line, using the chosed summary.stat. Note that this does not really make sense with perturbation type data, and will combine experiments and controls when doing the summary if run on a perturbation dataset.
summarizeMolecularProfiles(pSet, mDataType, cell.lines, features, summary.stat = c("mean", "median", "first", "last", "and", "or"), fill.missing = TRUE, summarize = TRUE, verbose = TRUE, binarize.threshold = NA, binarize.direction = c("less", "greater"))
pSet |
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mDataType |
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cell.lines |
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features |
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summary.stat |
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fill.missing |
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summarize |
A flag which when set to FALSE (defaults to TRUE) disables summarizing and returns the data unchanged as a ExpressionSet |
verbose |
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binarize.threshold |
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binarize.direction |
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matrix
An updated PharmacoSet with the molecular data summarized
per cell line.
data(GDSCsmall) GDSCsmall <- summarizeMolecularProfiles(GDSCsmall, mDataType = "rna", cell.lines=cellNames(GDSCsmall), summary.stat = 'median', fill.missing = TRUE, verbose=TRUE) GDSCsmall