setConfigElement: setConfigElement

In MPIIComputationalEpigenetics/epiRepeatR: epiRepeatR

Description

Set a configuration item to a given value

Usage

setConfigElement(name, value)

Arguments

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

Value

nothing of particular interest.

Options used by the package

n.processes = 0

Number of processes used during parallel computations.

rscript.exec = "Rscript"

Rscript executable.

species = "human"

The organism/taxon the analysis pertains to.

refFasta = MPII default location

The reference fasta file for repeat elements. See vignette for instructions on how they can be obtained.

aligner.bs = "bsmap"

Aligner used for mapping bisulfite sequencing reads to the repeat reference. Currently only "bsmap" is supported.

alignment.params.bs = "-g 3 -v 0.2"

Additional parameters appended during the command line call to the bisulfite aligner.

aligner.chip = "chip_bwa"

Aligner used for mapping ChIP-seq reads to the repeat reference. Currently only "chip_bwa" and "chip_bowtie2" are supported.

alignment.params.chip.bwa = "-t 8 -q 20"

Additional parameters appended during the command line call to the BWA ChIP-seq aligner.

alignment.params.chip.bowtie2 = "-t 8 -q 20"

Additional parameters appended during the command line call to the bowtie2 ChIP-seq aligner.

aligner.atac = "atac_bowtie2"

Aligner used for mapping ATAC-seq reads to the repeat reference. Currently only "atac_bowtie2" is supported.

alignment.params.atac.bowtie2 = "-t 8 -q 20"

Additional parameters appended during the command line call to the bowtie2 ATAC-seq aligner.

samtools.exec = "samtools"

Location of the samtools executable.

chip.mergeInput = FALSE

Flag indicating whether all bam files containing Input/WCE for ChIP-seq should be merged into one joint Input.

tempDir = tempdir()

Temporary directory for analysis. Specify to be the empty string ("") to create a temp directory in the analysis directory during runAnalysis.

inputBam.mappingStatus = "all"

Which reads should be extracted from the bam files and subsequently mapped to repetitive elements: Only reads also mapped in the source bam file ("mapped"), only reads unmapped in the source bam file ("unmapped"), or both ("all", default).

plotRepTree.dendroMethod = "repeatFamily"

Method for plotting the repeat subfamily dendrogram. Valid methods include grouping by repeat subfamily ("repeatFamily"), grouping by hierarchical clustering based on k-mer counts in the repeat sequence (Euclidean distance, complete linkage) ("hierClust"), grouping by hierarchical clustering based on occurrences of terms in the annotation fields of a repeat ("annotClust"; requires that the repeat references has been annotated from the EMBL format.)

plotRepTree.leafColorMethod = "coverage"

Method for coloring the leafs in the repeat subfamily dendrogram. Valid methods include: color by read coverage ("coverage"; default), color by genomic abundance (percent of bases covered; "abundance")

plotRepTree.normEnrich = "none"

Method for normalizing enrichment data before plotting. Currently supported are: none (no normalization), standard (subtract the mean, devide by standard deviation), scale (scale to the interval [0,1]) and quantile (Quantile normalization)

plotRepTree.meth.minCpGs = 2

Minimum number of CpGs to be contained in a repeat element in order to be shown in the resulting methylation tree plots.

plotRepTree.meth.minReads = 100

Minimum number of reads that must match to a given repeat element in order to be shown in the resulting methylation tree plots.

annotCols.replicates = NULL

Column names or indices in the annotation column used for replicate analysis (in exploratory report)

meth.minCpGcov = 5

Minimum number of reads covering a CpG in a repeat element in order to be considered in computing methylation.

meth.methCallFormat = "BisSNP"

Format of input methylation calling files. Can be one of "BisSNP", "EPP"

genomeRepeatTrack = NULL

Path to an RDS file containing a GenomeRepeatTrack object. These files are used to map the sequencing reads instead of the consensus reference. Only meaningful if processing input files of type genomeMethCalling or genomeAlignment.

debug = FALSE

Logical specifying whether the debug mode is enabled and additional debug-related output should be provided.

Author(s)

Fabian Mueller

MPIIComputationalEpigenetics/epiRepeatR documentation built on March 22, 2021, 11:09 p.m.