compareGroups | R Documentation |
Compares sets of individuals for reccuring mutations
compareGroups(
metaDataFile,
outputDirectories,
project,
subgroups1,
subgroups2,
name,
includeNormal = F,
clonalityCut = 0.4,
excludeSamples = c(),
excludeIndividuals = c(),
cosmicDirectory = "",
analysisName = "cohortAnalysis",
cpus = 1,
forceRedoVariants = F,
forceRedoMean = F,
forceRedoMeanPlot = F,
forceRedoMatrixPlot = F,
genome = "hg19",
ignoreCNAonly = F,
cnvWeight = 1
)
metaDataFile |
character: Path to the metaData. |
outputDirectories |
A named list of output directories, containing the entry Rdirectory and plotDirectory where the saved data and plots will be stored respectively. |
project |
character: The project containing the subgroups. |
name |
character: The name of the comparison. This names the output directory. |
clonalityCut |
numeric: the minimum required clonality to be included in the analysis. Deafult 0.4. |
cosmicDirectory |
character: The directory with the COSMIC data. |
cpus |
integer: The maximum number of parallel processes. |
forceRedoMean |
boolean: Force redo the mean CNAs ans SNVs rates over individuals. Default FALSE. |
forceRedoMeanPlot |
boolean: Force redo the mean CNA plot. Default FALSE. |
forceRedoMatrixPlot |
boolean: Force redo the hit matrix plot. Default FALSE. |
genome |
character: the genome being studied. Default "hg19". |
subgroup1 |
character: The first subgroup(s). |
subgroup2 |
character: The second subgroup(s). |
This function runs a cohort analysis, comparing two subgroups (within a project) to each other. See cohortAnalyseBatch for details.
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