Replacement of the classification slot in a SplitTypeRdata object

A function for replacement of the classification slot in a SplitTypeRdata class.

# S4 method for class 'SplitTypeRdata'
classification(x) <- value

Arguments

x

a SplitTypeRdata object.

value

NULL or a list of the classification data for each signature. The list should have one entry per signature.

Value

the modified SplitTypeRdata object when the new value is valid.

Author

Astrid Deschênes

Examples

## Two demo signatures
sign <- list("SignatureA"=c("EGFR", "CTTN", "ACTB"),
    "SignatureB"=c("ACTR2", "AKT1"))

## Create a SplitTypeRdata object with the signatures
demo <- new("SplitTypeRdata", signatures=sign)

## Create the classification of 3 samples for each signature
## Each entry contains the GSVA score of each sample and its
## classification (the signature name or "unclassified")
demoClass <- list()
demoClass[["SignatureA"]] <- data.frame(GSVA_score=c(0.45, -0.32, 0.12),
    classification=c("SignatureA", "unclassified", "unclassified"),
    row.names=c("Sample_1", "Sample_2", "Sample_3"))
demoClass[["SignatureB"]] <- data.frame(GSVA_score=c(-0.51, 0.38, 0.29),
    classification=c("unclassified", "SignatureB", "SignatureB"),
    row.names=c("Sample_1", "Sample_2", "Sample_3"))

## Assign the classification to the object
classification(demo) <- demoClass

## Get the classification for the first signature
classification(demo)[["SignatureA"]]
#>          GSVA_score classification
#> Sample_1       0.45     SignatureA
#> Sample_2      -0.32   unclassified
#> Sample_3       0.12   unclassified