getComparisonInfo: getComparisonInfo
In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

getComparisonInfo

R Documentation

getComparisonInfo

Description

retrieve the comparison information for an DsAcc object. Analogous to RnBeads::get.comparison.info

Usage

getComparisonInfo(
  dsa,
  cmpNames = NULL,
  regionTypes = getRegionTypes(dsa),
  allPairs = TRUE,
  adjPairCols = NULL,
  minGrpSize = 1L,
  maxGrpCount = NULL
)

Arguments

`dsa`	`DsAcc` object
`cmpNames`	column names of the sample annotation of the dataset that will be used for comparison
`regionTypes`	which region types should be processed for differential analysis.
`allPairs`	Logical indicating whether all pairwise comparisons should be conducted, when more than 2 groups are present
`adjPairCols`	argument passed on to `rnb.sample.groups`. See its documentation for details.
`minGrpSize`	Minimum number of samples required to form a group in comparison
`maxGrpCount`	maximum number of groups to consider for comparisons

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