qtlSetOption {MAGAR} | R Documentation

## qtlSetOption

### Description

Change global options for methQTL calculation

### Usage

    qtlSetOption(
      rnbeads.options = NULL,
      meth.data.type = "idat.dir",
      geno.data.type = "plink",
      rnbeads.report = "temp",
      rnbeads.qc = FALSE,
      hdf5dump = FALSE,
      hardy.weinberg.p = 0.001,
      db.snp.ref = NULL,
      minor.allele.frequency = 0.05,
      missing.values.samples = 0.05,
      plink.geno = 0.1,
      impute.geno.data = FALSE,
      n.prin.comp = NULL,
      plink.path = NULL,
      fast.qtl.path = NULL,
      bgzip.path = NULL,
      tabix.path = NULL,
      correlation.type = "pearson",
      cluster.cor.threshold = 0.25,
      standard.deviation.gauss = 250,
      absolute.distance.cutoff = 5e+05,
      linear.model.type = "classial.linear",
      representative.cpg.computation = "row.medians",
      meth.qtl.type = "oneVSall",
      max.cpgs = 40000,
      cluster.architecture = "sge",
      cluster.config = c(h_vmem = "5G", mem_free = "5G"),
      n.permutations = 1000,
      compute.cor.blocks = TRUE,
      recode.allele.frequencies = FALSE,
      vcftools.path = NULL,
      imputation.user.token = NULL,
      imputation.reference.panel = "apps@hrc-r1.1",
      imputation.phasing.method = "shapeit",
      imputation.population = "eur"
    )

### Arguments

`rnbeads.options` | Path to an XML file specifying the RnBeads options used for data import. The default options are suitable for Illumina Beads Array data sets.
`meth.data.type` | Type of DNA methylation data used. Choices are listed in `rnb.execute.import`.
`geno.data.type` | The type of data to be imported. Can be either `'plink'` for `'.bed', '.bim',` and `'.fam'` or `'.dos'` and `'txt'` files or `'idat'` for raw IDAT files.
`rnbeads.report` | Path to an existing directory, in which the preprocessing report of RnBeads is to be stored. Defaults to the temporary file.
`rnbeads.qc` | Flag indicating if the quality control module of RnBeads is to be executed.
`hdf5dump` | Flag indicating, if large matrices are to be stored on disk rather than in main memory using the `HDF5Array` package.
`hardy.weinberg.p` | P-value used for the markers to be excluded if they do not follow the Hardy-Weinberg equilibrium as implemented in `PLINK`.
`db.snp.ref` | Path to a locally stored version of dbSNP[3]. If this option is specified, the reference allele is determined from this file instead of from the allele frequencies of the dataset. This circumvents problems with some imputation methods. If `NULL`(default), recoding will not be performed.
`minor.allele.frequency` | Threshold for the minor allele frequency of the SNPs to be used in the analysis.
`missing.values.samples` | Threshold specifying how much missing values per SNP are allowed across the samples to be included in the analyis.
`plink.geno` | Threshold for missing values per SNP
`impute.geno.data` | Flag indicating if imputation of genotyping data is to be perfomed using the Michigan imputation server (https://imputationserver.sph.umich.edu/index.html)[2].
`n.prin.comp` | Number of principal components of the genetic data to be used as covariates in the methQTL calling. `NULL` means that no adjustment is conducted.
`plink.path` | Path to an installation of PLINK (also comes with the package)
`fast.qtl.path` | Path to an installation of fastQTL (comes with the package for Linux)
`bgzip.path` | Path to an installation of BGZIP (comes with the package for Linux)
`tabix.path` | Path to an installation of TABIX (comes with the package for Linux)
`correlation.type` | The type of correlation to be used. Please note that for `type='pearson'` (default) the more efficient implementation of correlation in the `bigstatsr` is used. Further available options are `'spearman'` and `'kendall'`.
`cluster.cor.threshold` | Threshold for CpG methylatin state correlation to be considered as connected in the distance graph used to compute the correlation clustering.
`standard.deviation.gauss` | Standard deviation of the Gauss distribution used to weight the correlation according to its distance.
`absolute.distance.cutoff` | Distance cutoff after which a CpG correlation is not considered anymore.
`linear.model.type` | Linear model type to be used. Can be either `"categorical.anova"` or `"classical.linear"`. If `'meth.qtl.type'='fastQTL'`, this option is automatically set to `'fastQTL'` see `callMethQTLBlock` for more informations.
`representative.cpg.computation` | Option specifying how reference CpGs per correlation block are to be computed. Available options are `"row.medians"` for the site that is the row median across the samples within the correlation block (for ties a random selection is performed), `"mean.center"` for an artifical site in the geometric center of the block with the average methylation level or `"best.all"` for the CpG with the best p-value across all of the CpGs in the correlation block.
`meth.qtl.type` | Option specifying how a methQTL interaction is computed. Since the package is based on correlation blocks, a single correlation block can be associated with either one SNP (`meth.qtl.type='oneVSall'`), with multiple SNPs (`meth.qtl.type='allVSall'`), or each correlation block can once be positively and once negatively correlated with a SNP genotype (`meth.qtl.type='twoVSall'`). Additionally, we provide the option to use (`FastQTL`)[1] as a methQTL mapping tool (option `'fastQTL'`).
`max.cpgs` | Maximum number of CpGs used in the computation (used to save memory). 40,000 is a reasonable default for machines with ~128GB of main memory. Should be smaller for smaller machines and larger for larger ones.
`cluster.architecture` | The type of HPC cluster architecture present. Currently supported are `'sge'` and `'slurm'`
`cluster.config` | Resource parameters needed to setup an SGE or SLURM cluster job. Includes `h_vmem` and `mem_free` for SGE and `clock.limit` and `mem.size` for SLURM. An example configuration for SLURM would be `c("clock.limit"="1-0","mem.size"="10G")` for 1 day of running time (format days:hours) and 10 GB of maximum memory usage. Additionally, `'n.cpus'` can be specified as the SLURM option `cpus-per-task`
`n.permutations` | The number of permutations used to correct the p-values for multiple testing. See (http://fastqtl.sourceforge.net/) for further information.
`compute.cor.blocks` | Flag indicating if correlation blocks are to be called. If `FALSE`, each CpG is considered separately.
`recode.allele.frequencies` | Flag indicating if the reference allele is to be redefined according to the frequenciess found in the cohort investigated.
`vcftools.path` | Path to the installation of VCFtools. Necessary is the vcf-sort function in this folder.
`imputation.user.token` | The user token that is required for authorization with the Michigan imputation server. Please have a look at https://imputationserver.sph.umich.edu, create a user account and request a user token for access in your user profile.
`imputation.reference.panel` | The reference panel used for imputation. Please see https://imputationserver.readthedocs.io/en/latest/reference-panels/ for further information which panels are supported by the Michigan imputation server.
`imputation.phasing.method` | The phasing method employed by the Michigan imputation server. See https://imputationserver.readthedocs.io/en/latest/api/ for further information.
`imputation.population` | The population for the phasing method required by the Michigan imputation server. See https://imputationserver.readthedocs.io/en/latest/api/ for further information.

### Value

None

### Author(s)

Michael Scherer

### References

1. Ongen, H., Buil, A., Brown, A. A., Dermitzakis, E. T., & Delaneau, O. (2016). Fast and efficient QTL mapper for thousands of molecular phenotypes. Bioinformatics, 32(10), 1479–1485. https://doi.org/10.1093/bioinformatics/btv722 2. Das S, Forer L, Schönherr S, Sidore C, Locke AE, et al. (2016). Next-generation genotype imputation service and methods. Nature Genetics 48, 1284–1287, https://doi.org/10.1038/ng.3656 3. Sherry, S. T. et al. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308–311, https://doi.org/10.1093/nar/29.1.308.

### Examples

    qtlGetOption("rnbeads.report")
    qtlSetOption(rnbeads.report=getwd())
    qtlGetOption("rnbeads.report")

[Package MAGAR version 1.0.1 Index]