Init AL object

Create an Alteration Landscape (AL) object

new.AL(am, samples.on.row = TRUE)

Arguments

am

= NULL The binary alteration matrix

samples.on.row

= TRUE Are samples on rows?

Value

An Alteration Landscape (AL) object with the gam

Examples

am = matrix(rbinom(50, 1, 0.1), ncol=5, nrow=10)
new.AL(am)
#> $am
#>           alteration_1 alteration_2 alteration_3 alteration_4 alteration_5
#> sample_1         FALSE        FALSE        FALSE        FALSE        FALSE
#> sample_2         FALSE        FALSE        FALSE        FALSE        FALSE
#> sample_3         FALSE        FALSE        FALSE        FALSE        FALSE
#> sample_4         FALSE        FALSE        FALSE        FALSE        FALSE
#> sample_5         FALSE        FALSE         TRUE        FALSE        FALSE
#> sample_6         FALSE        FALSE        FALSE        FALSE        FALSE
#> sample_7         FALSE        FALSE        FALSE        FALSE        FALSE
#> sample_8         FALSE        FALSE        FALSE         TRUE         TRUE
#> sample_9         FALSE        FALSE        FALSE        FALSE         TRUE
#> sample_10        FALSE         TRUE        FALSE        FALSE        FALSE
#> 
#> $alterations
#> $alterations$alteration.class
#> alteration_1 alteration_2 alteration_3 alteration_4 alteration_5 
#> "alteration" "alteration" "alteration" "alteration" "alteration" 
#> 
#> 
#> $samples
#> $samples$sample.class
#>  sample_1  sample_2  sample_3  sample_4  sample_5  sample_6  sample_7  sample_8 
#>  "sample"  "sample"  "sample"  "sample"  "sample"  "sample"  "sample"  "sample" 
#>  sample_9 sample_10 
#>  "sample"  "sample" 
#> 
#> 
#> attr(,"class")
#> [1] "AL"