backbone | R Documentation |
A module is a group of genes which, to some extent, shows the same expression behaviour. Several modules are connected together such that one or more genes from one module will regulate the expression of another module. By creating chains of modules, a dynamic behaviour in gene regulation can be created.
backbone(module_info, module_network, expression_patterns)
module_info |
A tibble containing meta information on the modules themselves.
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module_network |
A tibble describing which modules regulate which other modules.
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expression_patterns |
A tibble describing the expected expression pattern changes when a cell is simulated by dyngen. Each row represents one transition between two cell states.
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A dyngen backbone.
dyngen on how to run a dyngen simulation
library(tibble) backbone <- backbone( module_info = tribble( ~module_id, ~basal, ~burn, ~independence, "M1", 1, TRUE, 1, "M2", 0, FALSE, 1, "M3", 0, FALSE, 1 ), module_network = tribble( ~from, ~to, ~effect, ~strength, ~hill, "M1", "M2", 1L, 1, 2, "M2", "M3", 1L, 1, 2 ), expression_patterns = tribble( ~from, ~to, ~module_progression, ~start, ~burn, ~time, "s0", "s1", "+M1", TRUE, TRUE, 30, "s1", "s2", "+M2,+M3", FALSE, FALSE, 80 ) )
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