stateBrewer: Obtain combinatorial states from experiment table

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

This function computes combinatorial states from an experiment.table.

Usage

stateBrewer(
  experiment.table,
  mode,
  differential.states = FALSE,
  common.states = FALSE,
  exclusive.table = NULL,
  binary.matrix = NULL
)

Arguments

experiment.table	A data.frame specifying the experiment structure. See experiment.table.
mode	Mode of brewing. See Chromstar for a description of the parameter.
differential.states	A logical specifying whether differential states shall be returned.
common.states	A logical specifying whether common states shall be returned.
exclusive.table	A data.frame or tab-separated text file with columns 'mark' and 'group'. Histone marks with the same group will be treated as mutually exclusive.
binary.matrix	A logical matrix produced by dec2bin. If this is specified, only states specified by the rows of this matrix will be considered. The number of columns must match length(replicates) or length(statespec). Only for advanced use. No error handling for incorrect input.

Details

The binary modification state (unmodified=0 or modified=1) of multiple ChIP-seq samples defines a (decimal) combinatorial state such as:

	sample1	sample2	sample3	sample4	sample5	combinatorial state
bin1	0	0	1	0	0	4
bin2	0	0	0	0	0	0
bin3	0	1	0	1	0	10
bin4	0	1	1	1	1	15
bin5	0	0	1	0	1	5

Value

A data.frame with combinations and their corresponding (decimal) combinatorial states.

Author(s)

Aaron Taudt

Examples

## Construct an experiment table
data(experiment_table)
print(experiment_table)
## Construct combinatorial states
stateBrewer(experiment_table, mode='combinatorial')
stateBrewer(experiment_table, mode='differential')
stateBrewer(experiment_table, mode='full', common.states=TRUE)

## Exclude states with exclusive.table
excl <- data.frame(mark=c('H3K4me3','H3K27me3'),
                             group=c(1,1))
stateBrewer(experiment_table, mode='full', exclusive.table=excl)

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.