attractorToDataframe: Convert a BoolNet attractor to dataframe.

In mar-esther23/rgriffin: Gene Regulatory Interaction Formulator For Inquiring Networks

Description

If Booleans converts a BoolNet attractor to data frame with nodes displayed in Boolean format. First column is the attractor number, second is the number of state inside the attractor, the rest of the columns correspond to each node. If not Boolean it converts a BoolNet attractor to dataframe with properties as columns. The rownames correspond to the int value of each attractor, in the case of cycles the state are joined by sep. Each property of attr$attractors corresponds to a dataframe column. If the property has elements with length > 1 it converts them to a string and joins them with sep.

If Booleans converts a BoolNet attractor to data frame with nodes displayed in Boolean format. First column is the attractor number, second is the number of state inside the attractor, the rest of the columns correspond to each node. If not Boolean it converts a BoolNet attractor to dataframe with properties as columns. The rownames correspond to the int value of each attractor, in the case of cycles the state are joined by sep. Each property of attr$attractors corresponds to a dataframe column. If the property has elements with length > 1 it converts them to a string and joins them with sep.

Usage

attractorToDataframe(attr, sep = "/", node.names = NULL,
  Boolean = TRUE)

attractorToDataframe(attr, sep = "/", node.names = NULL,
  Boolean = TRUE)

Arguments

attr	BoolNet attractor object
sep	string to join elements with length > 1, default "/"
node.names	node names, by default taken from attractor object
Boolean	return attractor in Boolean or integer format, default FALSE
attr	BoolNet attractor object
node.names	node names, by default taken from attractor object
sep	string to join elements with length > 1, default "/"
Boolean	return attractor in Boolean or integer format, default FALSE

Value

If Boolean=TRUE return dataframe, each column corresponds to the numebr of attractor, state, or node. If Boolean=FALSE return dataframe, each column corresponds to a property of the attractor

If Boolean=TRUE return dataframe, each column corresponds to the numebr of attractor, state, or node. If Boolean=FALSE return dataframe, each column corresponds to a property of the attractor

Examples

attr <- getAttractors(cellcycle)
attractorToDataframe(attr)
#              involvedStates basinSize
#1                        162       512
#2 25/785/849/449/389/141/157       512

attractorToDataframe(attr, Boolean=TRUE)
#   attractor state CycD Rb E2F CycE CycA p27 Cdc20 Cdh1 UbcH10 CycB
#1         1     1    0  1   0    0    0   1     0    1      0    0
#2         2     1    1  0   0    1    1   0     0    0      0    0
#3         2     2    1  0   0    0    1   0     0    0      1    1
#4         2     3    1  0   0    0    1   0     1    0      1    1
#5         2     4    1  0   0    0    0   0     1    1      1    0
#6         2     5    1  0   1    0    0   0     0    1      1    0
#7         2     6    1  0   1    1    0   0     0    1      0    0
#8         2     7    1  0   1    1    1   0     0    1      0    0
attr <- getAttractors(cellcycle)
attractorToDataframe(attr)
#              involvedStates basinSize
#1                        162       512
#2 25/785/849/449/389/141/157       512

attractorToDataframe(attr, Boolean=TRUE)
#   attractor state CycD Rb E2F CycE CycA p27 Cdc20 Cdh1 UbcH10 CycB
#1         1     1    0  1   0    0    0   1     0    1      0    0
#2         2     1    1  0   0    1    1   0     0    0      0    0
#3         2     2    1  0   0    0    1   0     0    0      1    1
#4         2     3    1  0   0    0    1   0     1    0      1    1
#5         2     4    1  0   0    0    0   0     1    1      1    0
#6         2     5    1  0   1    0    0   0     0    1      1    0
#7         2     6    1  0   1    1    0   0     0    1      0    0
#8         2     7    1  0   1    1    1   0     0    1      0    0

mar-esther23/rgriffin documentation built on May 29, 2021, 10:03 p.m.