A small normalized expected gene counts matrix for 30 patients generated to be used as a demonstration set in this package.

Source: R/splitTypeR.R

A small normalized expected gene counts matrix for 30 patients generated to be used as a demonstration set in this package.

data(expNormalCountsDemo)

Format

a matrix containing normalized gene counts for 30 patients (columns). Only genes related to 2018 Tiriac PDAC PDO classical and basal-like signatures are present (row).

Value

a matrix containing normalized gene counts for 30 patients (columns). Only genes related to 2018 Tiriac PDAC PDO classical and basal-like signatures are present (row).

See also

  • runSubtypingBimodal for the classification of heterogeneous biological samples based on gene signature lists using a mixture of two normal distributions

  • getGeneSignaturesNames for the names of the available and ready-to-use gene signature lists

  • getGeneSignatures for the available and ready-to-use gene signature lists

Examples


## Load the demo normalized expected count matrix
data("expNormalCountsDemo")

## Load the demo signatures
data("signaturesDemo")

## Fix seed for reproducibility
set.seed(221)

## Run classification on the 30 patients using 25 permutations on 70% of 
## the cohort, and 10 points per patient for the up-scaling step
results <- runSubtypingBimodal(geneLists=signaturesDemo, 
    expectedCountsMatrix=expNormalCountsDemo, 
    permRatio=0.70, permNbr=25, upscaleNbr=10)
#> number of iterations= 79 
#> number of iterations= 80