PharmacoGx (version 1.1.6)

summarizeMolecularProfiles: Takes molecular data from a PharmacoSet, and summarises them into one entry per drug

Description

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.

Usage

summarizeMolecularProfiles(pSet, mDataType, cell.lines, features, summary.stat = c("mean", "median", "first", "last", "and", "or"), fill.missing = TRUE, summarize = TRUE, verbose = TRUE)

Arguments

pSet

PharmacoSet The PharmacoSet to summarize

mDataType

character which one of the molecular data types to use in the analysis, out of all the molecular data types available for the pset for example: rna, rnaseq, snp

cell.lines

character The cell lines to be summarized. If any cell.line has no data, missing values will be created

features

caracter A vector of the feature names to include in the summary

summary.stat

character which summary method to use if there are repeated cell.lines? Choices are "mean", "median", "first", or "last" In case molecular data type is mutation or fusion "and" and "or" choices are available

fill.missing

boolean should the missing cell lines not in the molecular data object be filled in with missing values?

summarize

A flag which when set to FALSE disables summarizing and returns the data unchanged as a ExpressionSet

verbose

boolean should messages be printed

Value

matrix An updated PharmacoSet with the molecular data summarized per cell line.

Examples

data(GDSCsmall)
GDSCsmall <- summarizeMolecularProfiles(GDSCsmall,
                    mDataType = "rna", cell.lines=cellNames(GDSCsmall),
                    summary.stat = 'median', fill.missing = TRUE, verbose=TRUE)
GDSCsmall