setConfigElement: setConfigElement
In demuellae/ChrAccR: Analyzing chromatin accessibility data in R

Description Usage Arguments Value Options used by the package Author(s)

Set a configuration item to a given value

1	setConfigElement(name, value)

`name`	name of the config item
`value`	value of the config item

nothing of particular interest.

tmpDir = temdir(): Directory for temporary files. Must be existing.
cleanMem = TRUE: During runtime, regularly clean-out the memory in order to reduce memory overuse
colorSchemes: named list of DISCRETE color schemes to be used for plotting. Each element should be a named vector specifying colors for groups/annotations.
colorSchemesCont: named list of CONTINOUS color schemes to be used for plotting. Each element should be a vector specifying a range of colors.
geneModelVersions: Gene model versions to be used for various genomes
regionTypes: Region types to be used in the analysis
chromVarRegionTypes = NULL: Region types to be used for chromVar analysis. If NULL (default), ChrAccR will automatically look for region types with the keyword "peak" in their name.
chromVarMotifs = "jaspar_vert": Character vector of names of TF motif sets to be used in ChromVAR analyses. By default the vertebrate set of the JASPAR database will be used.
chromVarMotifNamesForDimRed: Names of motifs to be used for dimension reduction plots in the reports. [only relevant for single-cell data]
annotationColumns: Sample annotation columns to be used for reporting
annotationMinGroupSize: Minimum size of a group to be used in the reports. Influences which annotation columns are selected for reporting.
doPeakCalling = FALSE: Perform per-sample peak calling and retrieve consensus peak set. Requires that macs2 is installed and can be called from the command line. [for bulk data analysis only]
annotationPeakGroupColumn: Annotation column to base the consensus peak set replication filtering on.
annotationPeakGroupAgreePerc = 1.0: Percent of samples that have to agree to identify consensus peaks. See getConsensusPeakSet for details.
filteringCovgCount = 1L: Minimum insertion count to filter count matrices by. See filterLowCovg,DsATAC-method for details. [for bulk data analysis only]
filteringCovgReqSamples = 0.75: Minimum required samples to apply low coverage filtering to. See filterLowCovg,DsATAC-method for details. [for bulk data analysis only]
filteringSexChroms = FALSE: Flag indicating whether to remove sex chromosomes.
filteringScMinFragmentsPerCell = 1000L: Minimum number of fragments per cell to retain a cell in the analysis. [for single-cell data analysis only]
filteringScMaxFragmentsPerCell = Inf: Maximum number of fragments allowed per cell to retain a cell in the analysis. [for single-cell data analysis only]
filteringScMinTssEnrichment = 6: Minimum TSS enrichment score per cell to retain a cell in the analysis. [for single-cell data analysis only]
normalizationMethod = "quantile": Normalization method to use for count normalization. Allowed methods include the ones listed in transformCounts,DsATAC-method. [for bulk data analysis only]
exploratoryLogNormCounts = TRUE: Should a log-normalization be applied in the exploratory plot sections of the reports (dimension reduction, heatmaps)
differentialColumns: Sample annotation columns to be used for differential testing and reporting
differentialCompNames: Comparison names from which comparison information is derived. Must be in the format of "$GRP1_NAME vs $GRP2_NAME [$ANNOTATION_COLUMN]".
differentialAdjColumns: Sample annotation columns to be adjusted for in differential testing
lolaDbPaths: Precomputed LOLA databases to be used for enrichment analysis. If NULL (default), ChrAccR will download an apropriate core database.
scIterativeLsiRegType: For single-cell analysis only: region type to be used for clustering and dimension reduction using iterative LSI. By default (NULL), ChrAccR will look for a region type named "tiling".
scIterativeLsiClusterResolution = 0.4: For single-cell analysis only: Cluster resolution to use for iterative LSI.