Training and Analysing Asynchronous Boolean Models


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Documentation for package ‘BTR’ version 1.2.4

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BTR-package BTR: A package for studying asynchronous Boolean models
amat_to_bm Convert adjacency matrix into BoolModel object
bm_to_amat Convert BoolModel into adjacency matrix
bm_to_df Convert BoolModel object into BoolNet readable data frame
bon_bmodel HSC Boolean Model from Bonzanni et al.
bon_istate Initial state from Bonzanni et al.
BoolModel An S4 class to represent a Boolean Model
BoolModel-class An S4 class to represent a Boolean Model
BTR BTR: A package for studying asynchronous Boolean models
calc_mscore Calculating Boolean model score wrt to a dataset
calc_roc Calculate precision, recall, f-score, accuracy and specificity
check_and Check if containing AND terms
compress_bmodel Compress BoolModel
decompress_bmodel Decompress BoolModel
decreate_boolmodel Decreate Boolean model
df_to_bm Convert a data frame into BoolModel object
emodel1 Example Boolean Model used in the vignette
emodel2 Example Boolean Model used in the vignette
emodel3 Example Boolean Model used in the vignette
eval_bool Evaluating Boolean rules
extract_term Extract Boolean terms
filter_dflist Filter columns of df in a list
gen_one_rmodel Generate a random Boolean model
gen_singlerule Generate random act and inh rule for a single gene
gen_two_rmodel Generate two random Boolean models with a specified number of steps apart
gen_two_rmodel_dag Generate two random DAG Boolean models with a specified number of steps apart
get_encodings Get corresponding encodings for compression or decompression.
grow_bmodel Add extra genes to a Boolean model
initialise_data Initialise data
initialise_model Initialise model
initialise_raw_data Initialise raw data
krum_bmodel Myeloid Boolean Model from Krumsiek et al.
krum_istate Initial state from Krumsiek et al.
man_dist Calculates pairwise Manhattan distances between two matrices
match_term Check for matching terms
minmod_internal Inner function of minimal modification of whole Boolean model
minmod_model Minimal modification of whole Boolean model
model_consensus Intersection of genes
model_dist Calculate distance between Boolean models
model_setdiff Find the set difference between two Boolean models
model_train Training Model
outgenysis_model Output a Boolean Model into Genysis readable format
outgraph_model Output a Boolean Model into Cytoscape & Gephi readable format
outstate_graph Generate state transition graph
plotBM Plot Boolean Model
printBM Print Boolean Model
rcpp_simulate Simulate a Boolean model.
rcpp_validate Calculating validation scores between two adjacency matrices
simulate_model Simulating Boolean model
unique_raw_data Remove raw data duplicated wrt to the model state
validate_adjmat Calculate true positive, true negative, false positive and false negative
vcat Verbose cat
which.random.min Pick a random minimum value
wilson_raw_data Raw single cell qRT-PCR expression data from Wilson et al.
wilson_raw_rnaseq Raw single cell RNAseq expression data from Wilson et al.
writeBM Write Boolean Model