export,mutex

Create an input file for MUTEX (ref: https://code.google.com/p/mutex/ )

export.mutex(
  x,
  filename = "tronco_to_mutex",
  filepath = "./",
  label.mutation = "SNV",
  label.amplification = list("High-level Gain"),
  label.deletion = list("Homozygous Loss")
)

Arguments

x

A TRONCO compliant dataset.

filename

The name of the file

filepath

The path where to save the file

label.mutation

The event type to use as mutation

label.amplification

The event type to use as amplification (can be a list)

label.deletion

The event type to use as amplification (can be a list)

Value

A MUTEX example matrix

Examples

data(crc_gistic)
dataset = import.GISTIC(crc_gistic)
#> *** Using full GISTIC: #dim  9  x  6 
#> *** GISTIC input format conversion started.
#> Converting input data to character for import speedup.
#> Creating  24 events for 6 genes 
#> Extracting "Homozygous Loss" events (GISTIC = -2) 
#> Extracting "Heterozygous Loss" events (GISTIC = -1) 
#> Extracting "Low-level Gain" events (GISTIC = +1) 
#> Extracting "High-level Gain" events (GISTIC = +2) 
#> Transforming events in TRONCO data types ..... 
#> *** Binding events for 4 datasets.
#> *** Data extracted, returning only events observed in at least one sample 
#>  Number of events: n = 7 
#>  Number of genes: |G| = 6 
#>  Number of samples: m = 9 
export.mutex(dataset)
#>        TCGA-A6-2670 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677
#> NRAS              0            0            0            0            0
#> CTNNB1            0            0            0            0            0
#> FBXW7             0            0            0            0            0
#> APC               0            0            0            0            0
#> KRAS              0            0            0            0            0
#> TP53              0            0            0            0            0
#>        TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-AA-3516
#> NRAS              0            0            0            0
#> CTNNB1            0            0            0            0
#> FBXW7             0            0            0            0
#> APC               0            0            0            0
#> KRAS              0            0            0            0
#> TP53              0            0            0            0