html_from_graph {TraRe} | R Documentation |
From input Gene Regulatory Network, an html is generated containing a table with driver to target phenotype dependent relationships. Brief summary containing drivers normalized xor sum, which is the ratio between drivers-targets connections present only in one of both phenotypes over all possible connections, and cliques, which are driver genes that are highly correlated (over a user-decision threshold), and may have been lost during the fitting process of the LINKER method.
html_from_graph( gpath = NULL, wpath = paste0(tempdir()), user_mode = TRUE, cliquesbool = TRUE, ... )
gpath |
path to the graph object ('refinedsumm.rds'). (RDS format) |
wpath |
writing path, where the html and txts file will be saved. (Default: temp directory) |
user_mode |
boolean indicating if this function is called from user or internaly. (Default: TRUE) |
cliquesbool |
indicating if cliques method should be added to the summary table. (Default: TRUE) |
... |
every argument you should pass to generatecliques() in case cliquesbool is TRUE. |
Html and txts containing the mentioned files.
## For this example, we are going to use a generated 'refinedsumm.rds' from the su2c dataset ## (see vignette of TraRe for more information), which is at the external data folder ## of this package. gpath <- paste0(system.file('extdata',package='TraRe'),'/refinedsumm.rds') wpath <- paste0(system.file('extdata',package='TraRe')) ## We are going to use the drivers dataset from the external data folder as well. ## For more information about generatecliques() please check the help page of it. dataset<-readRDS(paste0(system.file('extdata',package='TraRe') ,'/tfs_linker_example_eg.rds')) html_from_graph(gpath=gpath,wpath=wpath,dataset=dataset)