View source: R/cohortAnalyseBatch.R
runSummaryPostAnalysis | R Documentation |
runs analyses across all samples in the batch
runSummaryPostAnalysis(
Rdirectory,
plotDirectory,
metaDataFile,
genome,
resourceDirectory = "superFreqResources",
GoI = NA,
GoIakas = c(),
excludeIndividuals = c(),
excludeSamples = c(),
cpus = 1
)
Rdirectory |
character: path to the Rdirectory of the batch run. |
plotDirectory |
character: path to the plotDirectory of the batch run. |
metaDataFile |
character: path to the tab separated meta data file. |
genome |
character: The genome build. 'hg19', hg38' or 'mm10'. Default 'hg19' |
GoI |
character vector: The genes of interest to be highlighted in the analysis. Default NA uses genes that are mutated in the cohort that are also in COSMIC census or pathogenic in ClinVar. |
GoIakas |
named character vector: changes the displayed name of the GoI. For example c('BCL2L11'='BIM', 'BCL2L1'='BCLxL') to display the commonly used gene names BIM and BCLxL instead of the SYMBOL names BCL2L11 and BCL2L1 used by superFreq. Default c(). |
excludeIndividuals |
character vector: Exclude these individuals from the analysis. Default c(). |
excludeSamples |
character vector: Exclude these samples from the analysis. Default c(). |
cpus |
integer: maximum number of threads used. default 1. |
This function carries out a number analyses across the individuals analysed in the top level Rdirectory. The output is placed in the plotDirectory, in a subdirectory called cohortWide. Probably convenient to not name individuals "cohortWide", or that individual will have to share directory with these plots.
## Not run:
superFreq(metaDataFile='metaData.tsv',
Rdirectory='R',
plotDirectory='plots',
cpus=4,
genome='hg38')
runSummaryPostAnalysis(metaDataFile='metaData.tsv',
Rdirectory='R',
plotDirectory='plots',
cpus=4,
genome='hg38')
## End(Not run)
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