buildBitString: Build the final bit string vector and times vector based on a...

In saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Build the final bit string vector and times vector based on a list of optimised bit strings at different time points.

Description

This function takes as input a list of vectors (can be only one). Each vector represents an optimised bit string at a different time point (as returned by the gaBinary functions). The first optimised bit string have the same length as the model to be optimised. The length of the following vectors corresponds to the number of zeros found in the previous bitstring. For instance, the following list of bit strings bStrings = list(c(1,1,1,0,0,0), c(1,0,0)) is correct whereas bStrings = list(c(1,1,1,0,0,0), c(1,0)) is incorrect.

This function is used internally by computeScoreTN and simulateTN. It should not be used by a user in principle. However, it may be useful for post processing.

New in version 1.3.28.

Usage

buildBitString(bStrings)

Arguments

bStrings

a list of bit strings as returned by the optimisation at different time points.

Value

This function returns 2 components. The first one as explained in the description is a vector of same length as the first input vector in the bStrings argument. The second component is a vector that keeps track of the time point at which each bit was optimised (see example).

Author(s)

T. Cokelaer

Examples

# Considering the optimised bitstrings at T1, T2 and T3 to be c(1,1,0,1,0,0),
# c(0,1,0) and c(0,1), then we can build the overall bitStrings as follows:

res = buildBitString(list(c(1,1,0,1,0,0), c(0,1,0), c(0,1)))

# The results bit string is accessed through the bs field:
res$bs
#[1] 1 1 0 1 1 1

# and times at which each bit is activated with the bsTimes field:
res$bsTimes

# res$bsTimes = c(1,1,0,1,2,3)

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.