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SelectX main function from SelectSim to create alteration object with background model

Source: R/selectX_run.R
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,
  tau = 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.

tau

tau (fold change) 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 SelectSim object with background model and other info along with result table

Examples

# \donttest{
data(luad_run_data, package = "SelectSim")
result <- selectX(
  M                = luad_run_data$M,
  sample.class     = luad_run_data$sample.class,
  alteration.class = luad_run_data$alteration.class,
  n.cores          = 1,
  min.freq         = 10,
  n.permut         = 10,
  verbose          = FALSE
)
head(result$result)
#>              SFE_1 SFE_2         name support_1 support_2     freq_1    freq_2
#> KRAS - TP53   KRAS  TP53  KRAS - TP53       154       221 0.30677291 0.4402390
#> EGFR - KRAS   EGFR  KRAS  EGFR - KRAS        57       154 0.11354582 0.3067729
#> STK11 - TP53 STK11  TP53 STK11 - TP53        59       221 0.11752988 0.4402390
#> KRAS - STK11  KRAS STK11 KRAS - STK11       154        59 0.30677291 0.1175299
#> BRAF - KRAS   BRAF  KRAS  BRAF - KRAS        35       154 0.06972112 0.3067729
#> EGFR - STK11  EGFR STK11 EGFR - STK11        57        59 0.11354582 0.1175299
#>              overlap  w_overlap max_overlap freq_overlap r_overlap w_r_overlap
#> KRAS - TP53       49 35.8760174         154   0.31818182  97.00000   57.893605
#> EGFR - KRAS        0  0.0000000          57   0.00000000  29.00000   15.393877
#> STK11 - TP53      13  9.5456386          59   0.22033898  37.14286   21.589941
#> KRAS - STK11      28 25.9230769          59   0.47457627  30.28571   16.651885
#> BRAF - KRAS        2  0.9821429          35   0.05714286  17.85714    9.648078
#> EGFR - STK11       0  0.0000000          57   0.00000000  12.85714    7.342055
#>                     wES wFDR        nES mean_r_nES nFDR cum_freq nFDR2 type
#> KRAS - TP53  -15.568785    0 -13.378381 -2.1904042    0      375     0   ME
#> EGFR - KRAS  -10.885115    0  -9.381782 -1.5033326    0      211     0   ME
#> STK11 - TP53  -8.516608    0  -7.056645 -1.4599627    0      280     0   ME
#> KRAS - STK11   6.555723    0   5.192369  1.3633536    0      213     0   CO
#> BRAF - KRAS   -6.127742    0  -5.092674 -1.0350682    0      189     0   ME
#> EGFR - STK11  -5.191617    0  -4.524529 -0.6670879    0      116     0   ME
#>               FDR
#> KRAS - TP53  TRUE
#> EGFR - KRAS  TRUE
#> STK11 - TP53 TRUE
#> KRAS - STK11 TRUE
#> BRAF - KRAS  TRUE
#> EGFR - STK11 TRUE
# }