Module transdisrupt
[hide private]
[frames] | no frames]

Module transdisrupt

source code

Classes [hide private]
  ErrorLogger
  ExpressionSimilarityMatrix
The ExpressionSimilarityMatrix is basically an implementation of a matrix, that is suited for our purposes.
  KnockoutTranssysProgram
KnockoutTranssysProgram
Functions [hide private]
 
uniform_cmp(element1, element2) source code
 
link_scorefunc(promoter) source code
 
score_matrix(network, promoter_element_scorefunc)
compute a distance adjacency matrix in which entries connecting a regulator to a cognate regulatee contain a score value computed by the scorefunc on the promoter element.
source code
 
pathscore_matrix(tp, scorefunc, no_connection_default_value)
get cost matrix of a transsys network.
source code
 
adjacency_matrix_scorefunc(promoter) source code
 
adjacency_matrix(network) source code
 
gene_factor_dictionary(tp)
make a dictionary, where gene is the key and the product is the value, for easy and convenient access.
source code
 
identity_perturber(c, fn)
docu missing
source code
 
create_disruption_network(name, matrix_D, gene_order, decay_rate, a_spec, a_max, constit)
docu missing
source code
 
reconstructed_adjacency_matrix(matrix_E, gamma, sigma)
docu missing
source code
 
referencestate_concentration_matrix(network, timesteps)
docu missing
source code
 
knockout_concentration_matrix(knockout_network, ref_conc_matrix, timesteps)
compute a matrix of expression values obtained from single gene knockout networks.
source code
 
knockout_concentration_matrix_lsys(knockout_network, aux_network, lsys_lines, timesteps)
docu missing
source code
 
logratio_matrix(ref_conc_matrix, conc_matrix)
docu missing
source code
 
overlaps(net_a, net_b)
docu missing
source code
Function Details [hide private]

score_matrix(network, promoter_element_scorefunc)

source code 

compute a distance adjacency matrix in which entries connecting a regulator to a cognate regulatee contain a score value computed by the scorefunc on the promoter element. All other entries are None.

pathscore_matrix(tp, scorefunc, no_connection_default_value)

source code 

get cost matrix of a transsys network. Calculation rules are implemented in a generic score_function().

gene_factor_dictionary(tp)

source code 

make a dictionary, where gene is the key and the product is the value, for easy and convenient access. It also provides a more understandable code and prevents errors, which could occur when using indices.

knockout_concentration_matrix(knockout_network, ref_conc_matrix, timesteps)

source code 

compute a matrix of expression values obtained from single gene knockout networks. The matrix element m[i][j] contains the expression level of factor j observed in a network in which factor i is knocked out (by replacement with a nonfunc product in the encoding gene). Expression starts with the reference state, taken from ref_conc_matrix, and is carried out for timesteps timesteps.