xGSsimulator: Function to simulate gold standard negatives (GSN) given gold...

In Pi: Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Description

xGSsimulator is supposed to simulate gold standard negatives (GSN) given gold standard positives (GSP) and an input gene network. GSN targets are those after excluding GSP targets and their 1-order (by default) neighbors in the gene network.

Usage

xGSsimulator(
GSP,
population = NULL,
network = c("STRING_medium", "STRING_low", "STRING_high",
"STRING_highest",
"PCommonsUN_high", "PCommonsUN_medium")[c(1, 6)],
network.customised = NULL,
neighbor.order = 1,
verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata",
guid = NULL
)

Arguments

GSP	a vector containing Gold Standard Positives (GSP)
population	a vector containing population space in which gold standard negatives (GSN) will be considered. By default, it is NULL, meaning genes in the network will be used instead
network	the built-in network. Currently two sources of network information are supported: the STRING database (version 10) and the Pathways Commons database (version 7). STRING is a meta-integration of undirect interactions from the functional aspect, while Pathways Commons mainly contains both undirect and direct interactions from the physical/pathway aspect. Both have scores to control the confidence of interactions. Therefore, the user can choose the different quality of the interactions. In STRING, "STRING_highest" indicates interactions with highest confidence (confidence scores>=900), "STRING_high" for interactions with high confidence (confidence scores>=700), "STRING_medium" for interactions with medium confidence (confidence scores>=400), and "STRING_low" for interactions with low confidence (confidence scores>=150). For undirect/physical interactions from Pathways Commons, "PCommonsUN_high" indicates undirect interactions with high confidence (supported with the PubMed references plus at least 2 different sources), "PCommonsUN_medium" for undirect interactions with medium confidence (supported with the PubMed references). By default, "STRING_medium" and "PCommonsUN_medium" are used
network.customised	an object of class "igraph". By default, it is NULL. It is designed to allow the user analysing their customised network data that are not listed in the above argument 'network'. This customisation (if provided) has the high priority over built-in network
neighbor.order	an integer giving the order of the neighborhood. By default, it is 1-order neighborhood
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display
RData.location	the characters to tell the location of built-in RData files. See xRDataLoader for details
guid	a valid (5-character) Global Unique IDentifier for an OSF project. See xRDataLoader for details

Value

a list with following components:

• GSN: a vector containing simulated GSN

• GSP: a vector containing GSP after considering the population space

• g: an "igraph" object

Note

If multiple graphs are provided, they will be unionised for use.

See Also

xDefineNet

Examples

RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run: 
sGS <- xGSsimulator(GSP, population=NULL,
network=c("STRING_medium","PCommonsUN_medium"),
RData.location=RData.location)

## End(Not run)

Pi documentation built on Nov. 29, 2021, 3 p.m.