runSummaryPostAnalysis: runs analyses across all samples in the batch

In ChristofferFlensburg/superFreq: Calls and tracks CNAs, SNVs and clones over multiple cancer exomes.

runs analyses across all samples in the batch

Description

runs analyses across all samples in the batch

Usage

runSummaryPostAnalysis(
  Rdirectory,
  plotDirectory,
  metaDataFile,
  genome,
  resourceDirectory = "superFreqResources",
  GoI = NA,
  GoIakas = c(),
  excludeIndividuals = c(),
  excludeSamples = c(),
  cpus = 1
)

Arguments

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.

Details

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.

Examples

## 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)

ChristofferFlensburg/superFreq documentation built on Nov. 15, 2023, 6:15 a.m.