In montilab/CaDrA: Candidate Driver Analysis

knitr::opts_chunk$set(message=FALSE, collapse = TRUE, comment="")

# R packages
library(SummarizedExperiment)
library(pheatmap)
library(devtools)
load_all()

The CaDrA package currently supports four scoring functions to search for subsets of genomic features that are likely associated with a specific outcome of interest (e.g., protein expression, pathway activity, etc.)

Kolmogorov-Smirnov Method (ks)
Conditional Mutual Information Method (revealer)
Wilcoxon Rank-Sum Method (wilcox)
Custom - An User Defined Scoring Method (custom)

Below, we run candidate_search() over the top 3 starting features using each of the four scoring functions described above.

Important Note:

The legacy or deprecated function topn_eval() is equivalent to the new and recommended candidate_search() function

Load packages

library(CaDrA)
library(pheatmap)
library(SummarizedExperiment)

Load required datasets

A binary features matrix also known as Feature Set (such as somatic mutations, copy number alterations, chromosomal translocations, etc.) The 1/0 row vectors indicate the presence/absence of ‘omics’ features in the samples. The Feature Set can be a matrix or an object of class SummarizedExperiment from SummarizedExperiment package)
A vector of continuous scores (or Input Scores) representing a functional response of interest (such as protein expression, pathway activity, etc.)

# Load pre-computed feature set
data(sim_FS)

# Load pre-computed input scores
data(sim_Scores)

Heatmap of simulated feature set

The simulated dataset, sim_FS, comprises of 1000 genomic features and 100 sample profiles. There are 10 left-skewed (i.e. True Positive or TP) and 990 uniformly-distributed (i.e. True Null or TN) features simulated in the dataset. Below is a heatmap of the first 100 features.

mat <- SummarizedExperiment::assay(sim_FS)
pheatmap::pheatmap(mat[1:100, ], color = c("white", "red"), cluster_rows = FALSE, cluster_cols = FALSE)

Search for a subset of genomic features that are likely associated with a functional response of interest using four scoring methods

1. Kolmogorov-Smirnov Scoring Method

See ?ks_rowscore for more details

ks_topn_l <- CaDrA::candidate_search(
  FS = sim_FS,
  input_score = sim_Scores,
  method = "ks_pval",          # Use Kolmogorow-Smirnow scoring function 
  method_alternative = "less", # Use one-sided hypothesis testing
  weights = NULL,              # If weights is provided, perform a weighted-KS test
  search_method = "both",      # Apply both forward and backward search
  top_N = 3,                   # Evaluate top 3 starting points for the search
  max_size = 10,               # Allow at most 10 features in meta-feature matrix
  do_plot = FALSE,             # We will plot it AFTER finding the best hits
  best_score_only = FALSE      # Return all results from the search
)

# Now we can fetch the feature set of top N features that corresponded to the best scores over the top N search
ks_topn_best_meta <- topn_best(ks_topn_l)

# Visualize best meta-feature result
meta_plot(topn_best_list = ks_topn_best_meta)

2. Wilcoxon Rank-Sum Scoring Method

See ?wilcox_rowscore for more details

wilcox_topn_l <- CaDrA::candidate_search(
  FS = sim_FS,
  input_score = sim_Scores,
  method = "wilcox_pval",      # Use Wilcoxon Rank-Sum scoring function
  method_alternative = "less", # Use one-sided hypothesis testing
  search_method = "both",      # Apply both forward and backward search
  top_N = 3,                   # Evaluate top 3 starting points for the search
  max_size = 10,               # Allow at most 10 features in meta-feature matrix
  do_plot = FALSE,             # We will plot it AFTER finding the best hits
  best_score_only = FALSE      # Return all results from the search
)

# Now we can fetch the feature set of top N feature that corresponded to the best scores over the top N search
wilcox_topn_best_meta <- topn_best(topn_list = wilcox_topn_l)

# Visualize best meta-feature result
meta_plot(topn_best_list = wilcox_topn_best_meta)

3. Conditional Mutual Information Scoring Method

See ?revealer_rowscore for more details

revealer_topn_l <- CaDrA::candidate_search(
  FS = sim_FS,
  input_score = sim_Scores,
  method = "revealer",         # Use REVEALER's CMI scoring function
  search_method = "both",      # Apply both forward and backward search
  top_N = 3,                   # Evaluate top 3 starting points for the search
  max_size = 10,               # Allow at most 10 features in meta-feature matrix
  do_plot = FALSE,             # We will plot it AFTER finding the best hits
  best_score_only = FALSE      # Return all results from the search
)

# Now we can fetch the ESet of top feature that corresponded to the best scores over the top N search
revealer_topn_best_meta <- topn_best(topn_list = revealer_topn_l)

# Visualize best meta-feature result
meta_plot(topn_best_list = revealer_topn_best_meta)

4. Custom - An User Defined Scoring Method

See ?custom_rowscore for more details

# A customized function using ks-test
customized_ks_rowscore <- function(FS, input_score, meta_feature=NULL, alternative="less", metric="pval"){

  # Check if meta_feature is provided
  if(!is.null(meta_feature)){
    # Getting the position of the known meta features
    locs <- match(meta_feature, row.names(FS))

    # Taking the union across the known meta features
    if(length(meta_feature) > 1) {
      meta_vector <- as.numeric(ifelse(colSums(FS[meta_feature,]) == 0, 0, 1))
    }else{
      meta_vector <- as.numeric(FS[meta_feature,])
    }

    # Remove the meta features from the binary feature matrix
    # and taking logical OR btw the remaining features with the meta vector
    FS <- base::sweep(FS[-locs, , drop=FALSE], 2, meta_vector, `|`)*1

    # Check if there are any features that are all 1s generated from
    # taking the union between the matrix
    # We cannot compute statistics for such features and thus they need
    # to be filtered out
    if(any(rowSums(FS) == ncol(FS))){
      warning("Features with all 1s generated from taking the matrix union ",
              "will be removed before progressing...\n")
      FS <- FS[rowSums(FS) != ncol(FS), , drop=FALSE]
    }
  }

  # KS is a ranked-based method
  # So we need to sort input_score from highest to lowest values
  input_score <- sort(input_score, decreasing=TRUE)

  # Re-order the matrix based on the order of input_score
  FS <- FS[, names(input_score), drop=FALSE]  

  # Compute the scores using the KS method
  ks <- apply(FS, 1, function(r){ 
    x = input_score[which(r==1)]; 
    y = input_score[which(r==0)];
    res <- ks.test(x, y, alternative=alternative)
    return(c(res$statistic, res$p.value))
  })

  # Obtain score statistics
  stat <- ks[1,]

  # Obtain p-values and change values of 0 to the machine lowest value 
  # to avoid taking -log(0)
  pval <- ks[2,]
  pval[which(pval == 0)] <- .Machine$double.xmin

  # Compute the -log(pval)
  # Make sure scores has names that match the row names of FS object
  pval <- -log(pval)

  # Determine which metric to returned the scores
  if(metric == "pval"){
    scores <- pval
  }else{
    scores <- stat
  }

  names(scores) <- rownames(FS)

  return(scores)

}

# Search for best features using a custom-defined function
custom_topn_l <- CaDrA::candidate_search(
  FS = SummarizedExperiment::assay(sim_FS),
  input_score = sim_Scores,
  method = "custom",                        # Use custom scoring function
  custom_function = customized_ks_rowscore, # Use a customized scoring function
  custom_parameters = NULL,                 # Additional parameters to pass to custom_function
  search_method = "both",                   # Apply both forward and backward search
  top_N = 3,                                # Evaluate top 3 starting points for the search
  max_size = 10,                            # Allow at most 10 features in meta-feature matrix
  do_plot = FALSE,                          # We will plot it AFTER finding the best hits
  best_score_only = FALSE                   # Return all results from the search
)

# Now we can fetch the feature set of top N feature that corresponded to the best scores over the top N search
custom_topn_best_meta <- topn_best(topn_list = custom_topn_l)

# Visualize best meta-feature result
meta_plot(topn_best_list = custom_topn_best_meta)