Description Usage Arguments Value Note See Also Examples
xDefineNet
is supposed to define a gene network sourced from the
STRING database or the Pathway Commons database. It returns an object
of class "igraph".
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | xDefineNet(network = c("STRING_highest", "STRING_high",
"STRING_medium",
"STRING_low", "PCommonsUN_high", "PCommonsUN_medium",
"PCommonsDN_high",
"PCommonsDN_medium", "PCommonsDN_Reactome", "PCommonsDN_KEGG",
"PCommonsDN_HumanCyc", "PCommonsDN_PID", "PCommonsDN_PANTHER",
"PCommonsDN_ReconX", "PCommonsDN_TRANSFAC", "PCommonsDN_PhosphoSite",
"PCommonsDN_CTD", "KEGG", "KEGG_metabolism", "KEGG_genetic",
"KEGG_environmental", "KEGG_cellular", "KEGG_organismal",
"KEGG_disease",
"REACTOME", "TRRUST"), STRING.only = c(NA, "neighborhood_score",
"fusion_score", "cooccurence_score", "coexpression_score",
"experimental_score", "database_score", "textmining_score")[1],
weighted = FALSE, verbose = TRUE,
RData.location = "http://galahad.well.ox.ac.uk/bigdata")
|
network |
the built-in network. Currently two sources of network information are supported: the STRING database (version 10) and the Pathway 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). For direct (pathway-merged) interactions from Pathways Commons, "PCommonsDN_high" indicates direct interactions with high confidence (supported with the PubMed references plus at least 2 different sources), and "PCommonsUN_medium" for direct interactions with medium confidence (supported with the PubMed references). In addition to pooled version of pathways from all data sources, the user can also choose the pathway-merged network from individual sources, that is, "PCommonsDN_Reactome" for those from Reactome, "PCommonsDN_KEGG" for those from KEGG, "PCommonsDN_HumanCyc" for those from HumanCyc, "PCommonsDN_PID" for those froom PID, "PCommonsDN_PANTHER" for those from PANTHER, "PCommonsDN_ReconX" for those from ReconX, "PCommonsDN_TRANSFAC" for those from TRANSFAC, "PCommonsDN_PhosphoSite" for those from PhosphoSite, and "PCommonsDN_CTD" for those from CTD. For direct (pathway-merged) interactions sourced from KEGG, it can be 'KEGG' for all, 'KEGG_metabolism' for pathways grouped into 'Metabolism', 'KEGG_genetic' for 'Genetic Information Processing' pathways, 'KEGG_environmental' for 'Environmental Information Processing' pathways, 'KEGG_cellular' for 'Cellular Processes' pathways, 'KEGG_organismal' for 'Organismal Systems' pathways, and 'KEGG_disease' for 'Human Diseases' pathways. 'REACTOME' for protein-protein interactions derived from Reactome pathways. 'TRRUST' for TRRUST curated TF-target relations |
STRING.only |
the further restriction of STRING by interaction type. If NA, no such restriction. Otherwide, it can be one or more of "neighborhood_score","fusion_score","cooccurence_score","coexpression_score","experimental_score","database_score","textmining_score". Useful options are c("experimental_score","database_score"): only experimental data (extracted from BIND, DIP, GRID, HPRD, IntAct, MINT, and PID) and curated data (extracted from Biocarta, BioCyc, GO, KEGG, and Reactome) are used |
weighted |
logical to indicate whether edge weights should be considered. By default, it sets to false. If true, it only works for the network from the STRING database |
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 |
an object of class "igraph"
The input graph will treat as an unweighted graph if there is no 'weight' edge attribute associated with
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | ## Not run:
# Load the library
library(XGR)
## End(Not run)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run:
# STRING (high quality)
g <- xDefineNet(network="STRING_high", RData.location=RData.location)
# STRING (high quality), with edges weighted
g <- xDefineNet(network="STRING_high", weighted=T,
RData.location=RData.location)
# STRING (high quality), only edges sourced from experimental or curated data
g <- xDefineNet(network="STRING_high",
STRING.only=c("experimental_score","database_score"),
RData.location=RData.location)
# Pathway Commons
g <- xDefineNet(network="PCommonsDN_medium",
RData.location=RData.location)
# KEGG (all)
g <- xDefineNet(network="KEGG", RData.location=RData.location)
# KEGG ('Organismal Systems')
g <- xDefineNet(network="KEGG_organismal",
RData.location=RData.location)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.