html_from_graph {TraRe}R Documentation

Html generation

Description

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.

Usage

html_from_graph(
  gpath = NULL,
  wpath = paste0(tempdir()),
  user_mode = TRUE,
  cliquesbool = TRUE,
  ...
)

Arguments

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.

Value

Html and txts containing the mentioned files.

Examples


## 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)



[Package TraRe version 1.1.0 Index]