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)