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SelectX main function to create alteration object with background model

selectX.Rd

selectX() takes a list object which consist of genome alteration matrix and tumor mutation burden.

Usage

selectX(
  M,
  sample.class,
  alteration.class,
  n.cores = 1,
  min.freq = 10,
  n.permut = 1000,
  lambda = 0.3,
  tao = 1,
  save.object = FALSE,
  folder = "./",
  verbose = TRUE,
  estimate_pairwise = FALSE,
  maxFDR = 0.25,
  seed = 42
)

Arguments

M

a list data object which consist of gams and tmbs.

sample.class

sample covariates as named list.

alteration.class

alteration covariates as named list.

n.cores

no of cores.

min.freq

number of samples for features to be atleast mutated in.

n.permut

number of simulations.

lambda

lambda parameter.

tao

tao parameter.

save.object

store the SelectX object.

folder

folder path to store the results.

verbose

print the time and each steps.

estimate_pairwise

Compute pairwise p-value

maxFDR

FDR value

seed

a random seed

Value

result a SelectX object with background model and other info along with result table