| stateBrewer {chromstaR} | R Documentation |
This function computes combinatorial states from an experiment.table.
stateBrewer( experiment.table, mode, differential.states = FALSE, common.states = FALSE, exclusive.table = NULL, binary.matrix = NULL )
experiment.table |
A |
mode |
Mode of brewing. See |
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 |
binary.matrix |
A logical matrix produced by |
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 |
A data.frame with combinations and their corresponding (decimal) combinatorial states.
Aaron Taudt
## 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)