hallmarks: Retrieve hallmarks of cancer count for genes

In glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

Description

Retrieve hallmarks of cancer count for genes

Usage

hallmarks(
  genes,
  metric = "count",
  hierarchy = "full",
  generate.plot = TRUE,
  show.message = FALSE
)

Arguments

genes	gene names
metric	see below
hierarchy	see below
generate.plot	flag to indicate if return object has a ggplot2 object
show.message	flag to indicate if run.cache method shows messages

Value

data.frame with choosen metric and hierarchy It also returns a vector with genes that do not have any hallmarks.

See http://chat.lionproject.net/api for more details on the metric and hallmarks parameters

To standardize the colors in the gradient you can use scale_fill_gradientn(limits=c(0,1), colours=topo.colors(3)) to limit between 0 and 1 for cprob and -1 and 1 for npmi

Examples

## Not run: 
    hallmarks(c('MOB1A', 'RFLNB', 'SPIC'))
    hallmarks(c('MOB1A', 'RFLNB', 'SPIC'), metric = 'cprob')

## End(Not run)

glmSparseNet documentation built on April 14, 2021, 6 p.m.