# Training and Analysing Asynchronous Boolean Models

## Documentation for package ‘BTR’ version 1.2.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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