get.comparison.info {RnBeads} | R Documentation

## get.comparison.info

### Description

retrieve the comparison information for an RnBSet object

### Usage

    get.comparison.info(x,
      pheno.cols = rnb.getOption("differential.comparison.columns"),
      region.types = rnb.region.types.for.analysis(x),
      pheno.cols.all.pairwise = rnb.getOption("differential.comparison.columns.all.pairwise"),
      columns.pairs = rnb.getOption("columns.pairing"),
      columns.adj = rnb.getOption("covariate.adjustment.columns"),
      adjust.sva = rnb.getOption("differential.adjustment.sva"),
      pheno.cols.adjust.sva = rnb.getOption("inference.targets.sva"),
      adjust.celltype = rnb.getOption("differential.adjustment.celltype"),
      adjust.na.rm = TRUE)

### Arguments

`x` | `RnBSet` object
`pheno.cols` | column names of the pheno slot in `x` on which the dataset should be partitioned. Those columns are required to be factors or logical. In case of factors, each group in turn will be compared to all other groups
`region.types` | which region types should be processed for differential methylation
`pheno.cols.all.pairwise` | integer or character vector specifying the colomns of `pheno(x)` on which all pairwise comparisons should be conducted. A value of `NULL` indicates no columns.
`columns.pairs` | argument passed on to `rnb.sample.groups`. See its documentation for details.
`columns.adj` | Column names or indices in the table of phenotypic information to be used for confounder adjustment in the differential methylation analysis.
`adjust.sva` | flag indicating whether the adjustment table should also contain surrogate variables (SVs) for the given target variable.
`pheno.cols.adjust.sva` | Target variables for SVA adjustment. Only important if `adjust.sva==TRUE`. Only the intersection of `pheno.cols` and `pheno.cols.adjust.sva` is considered for SVA adjustment.
`adjust.celltype` | flag indicating whether the resulting table should also contain estimated celltype contributions. See `rnb.execute.ct.estimation` for details.
`adjust.na.rm` | Flag indicating whether NAs in the adjustment table should be removed.

### Value

a list containing one element for each comparison to be conducted. Each element is again a list containing:

`comparison`

  the name of the comparison

`pheno.colname`

  the column name of the sample annotation table the comparison is derived from

`group.names`

  the names of the two groups being compared

`group.inds`

  the sample indices of the samples belonging to the two groups

`paired`

  flag indicating whether paired analysis is conducted

`adj.sva`

  flag indicating whether adjustment for SVA is conducted

`adj.celltype`

  flag indicating whether adjustment for cell type is conducted

`adjustment.table`

  the covariate adjustment table. `NULL` if the comparison is not adjusted

`region.types`

  the region types applicable to the analysis

### Author(s)

Fabian Mueller

### Examples

    library(RnBeads.hg19)
    data(small.example.object)
    logger.start(fname=NA)
    cmp.info <- get.comparison.info(rnb.set.example,pheno.cols=c("Sample_Group","Treatment"))
    cmp.info[[1]]

[Package RnBeads version 1.12.1 Index]