Build the full interaction results table from selectX outputs

Usage

interaction.table(
  al,
  als,
  obs,
  wobs,
  r.obs = NULL,
  r.wobs = NULL,
  null,
  maxFDR = 0.2,
  n.cores = 1,
  estimate_pairwise = FALSE,
  n.permut = 1000
)

Arguments

al: Alteration landscape object (al$am, etc.)
als: Alteration landscape stats (from al.stats)
obs: Observed pairwise overlap matrix
wobs: Weighted observed pairwise overlap matrix
r.obs: List of null model overlap matrices
r.wobs: List of null model weighted overlap matrices
null: Null model list (simulated binary matrices)
maxFDR: FDR cutoff for calling significant results
n.cores: Number of cores
estimate_pairwise: Whether to compute per-pair empirical p-values
n.permut: Number of permutations

Value

Data frame with one row per gene pair and columns for overlap, effect sizes, FDR, and interaction type.

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
# }