getComparisonTable-DsAcc-method: getComparisonTable-methods
In GreenleafLab/ChrAccR: Analyzing chromatin accessibility data in R

getComparisonTable,DsAcc-method

R Documentation

getComparisonTable-methods

Description

Retrieve a table describing pairwise comparisons on a DsAcc object

Usage

## S4 method for signature 'DsAcc'
getComparisonTable(
  .object,
  cols = NULL,
  cols1vAll = NULL,
  compNames = NULL,
  minGroupSize = 2L,
  maxGroupCount = length(.object) - 1
)

Arguments

`.object`	`DsAcc` object
`cols`	column names in the sample annotation table to consider for pairwise comparisons
`cols1vAll`	column names in the sample annotation table to consider for 1-vs-all comparisons
`compNames`	vector of character strings specifying a fixed comparison names to be parsed (format "$GRP1_NAME vs $GRP1_NAME [$ANNOTATION_COLUMN]")
`minGroupSize`	Minimum size of a group to be used in comparison. Affects the annotation columns that will be used for comparisons.
`maxGroupCount`	Maximum number of groups for a column to be considered for comparison.

Value

a data.frame with comparison inforamtion containing columns for the comparison name (compName), column in the annotation table (compCol) and group names for the two groups in the comparison (grp1Name, grp2Name),