state.brewer: Obtain combinatorial states from specification

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

Description

This function returns all combinatorial (decimal) states that are consistent with a given abstract specification.

Usage

state.brewer(
  replicates = NULL,
  differential.states = FALSE,
  min.diff = 1,
  common.states = FALSE,
  conditions = NULL,
  tracks2compare = NULL,
  sep = "+",
  statespec = NULL,
  diffstatespec = NULL,
  exclusive.table = NULL,
  binary.matrix = NULL
)

Arguments

replicates	A vector specifying the replicate structure. Similar entries will be treated as replicates.
differential.states	A logical specifying whether differential states shall be returned.
min.diff	The minimum number of differences between conditions.
common.states	A logical specifying whether common states shall be returned.
conditions	A vector with the same length as replicates. Similar entries will be treated as belonging to the same condition. Usually your tissue or cell types or time points.
tracks2compare	A vector with the same length as replicates. This vector defines the tracks between which conditions are compared. Usually your histone marks.
sep	Separator used to separate the tracknames in the combinations. The default '+' should not be changed because it is assumed in follow-up functions.
statespec	If this parameter is specified, replicates will be ignored. A vector composed of any combination of the following entries: '0.[]', '1.[]', 'x.[]', 'r.[]', where [] can be any string. '0.A': sample A is 'unmodified' '1.B': sample B is 'modified' 'x.C': sample C can be both 'unmodified' or 'modified' 'r.D': all samples in group D have to be in the same state 'r.[]': all samples in group [] have to be in the same state
diffstatespec	A vector composed of any combination of the following entries: 'x.[]', 'd.[]', where [] can be any string. 'x.A': sample A can be both 'unmodified' or 'modified' 'd.B': at least one sample in group B has to be different from the other samples in group A 'd[]': at least one sample in group [] has to be different from the other samples in group []
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, David Widmann

Examples

# Get all combinatorial states where sample1=0, sample2=1, sample3=(0 or 1),
#  sample4=sample5
chromstaR:::state.brewer(statespec=c('0.A','1.B','x.C','r.D','r.D'))

# Get all combinatorial states where sample1=sample2=sample3, sample4=sample5
chromstaR:::state.brewer(statespec=c('r.A','r.A','r.A','r.B','r.B'))

# Get all combinatorial states where sample1=sample5, sample2=sample3=1,
#  sample4=(0 or 1)
chromstaR:::state.brewer(statespec=c('r.A','1.B','1.C','x.D','r.A'))

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