hallmarks {glmSparseNet} | R Documentation

## Retrieve hallmarks of cancer count for genes

### 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)

[Package glmSparseNet version 1.8.1 Index]