feat: Updated src/Snps/SNPs.php

src/Snps/SNPs.php

@@ -41,9 +41,9 @@ class SNPs implements Countable, Iterator
     private array $_duplicate = [];
     private array $_discrepant_XY = [];
     private array $_heterozygous_MT = [];
-
-
-    /**
+    private DataFrame $dataFrame;
+    private SNPAnalysis $snpAnalysis;
+    private MathOperations $mathOperations;
 
     /**
      * SNPs constructor.
@@ -96,6 +96,9 @@ public function __construct(
                 // $this->_parallelizer = new Parallelizer($parallelize, $processes);
                 $this->_cluster = "";
                 $this->_chip = "";
+        $this->dataFrame = new DataFrame();
+        $this->snpAnalysis = new SNPAnalysis();
+        $this->mathOperations = new MathOperations();
                 $this->_chip_version = "";
 
                 $this->ensemblRestClient = $ensemblRestClient ?? new Ensembl("https://api.ncbi.nlm.nih.gov", 1);
@@ -2971,3 +2974,93 @@ public function matchWith(SNPs $otherKit): SNPs
 
 
 // }
+    /**
+     * Computes cluster overlap based on given threshold.
+     *
+     * @param float $cluster_overlap_threshold The threshold for cluster overlap.
+     * @return array The computed cluster overlap DataFrame.
+     */
+    public function computeClusterOverlap($cluster_overlap_threshold = 0.95): array {
+        // Sample data for cluster overlap computation
+        $data = [
+            "cluster_id" => ["c1", "c3", "c4", "c5", "v5"],
+            "company_composition" => [
+                "23andMe-v4",
+                "AncestryDNA-v1, FTDNA, MyHeritage",
+                "23andMe-v3",
+                "AncestryDNA-v2",
+                "23andMe-v5, LivingDNA",
+            ],
+            "chip_base_deduced" => [
+                "HTS iSelect HD",
+                "OmniExpress",
+                "OmniExpress plus",
+                "OmniExpress plus",
+                "Illumina GSAs",
+            ],
+            "snps_in_cluster" => array_fill(0, 5, 0),
+            "snps_in_common" => array_fill(0, 5, 0),
+        ];
+
+        // Create a DataFrame from the data and set "cluster_id" as the index
+        $df = new DataFrame($data);
+        $df->setIndex("cluster_id");
+
+        $to_remap = null;
+        if ($this->build != 37) {
+            // Create a clone of the current object for remapping
+            $to_remap = clone $this;
+            $to_remap->remap(37); // clusters are relative to Build 37
+            $self_snps = $to_remap->snps()->select(["chrom", "pos"])->dropDuplicates();
+        } else {
+            $self_snps = $this->snps()->select(["chrom", "pos"])->dropDuplicates();
+        }
+
+        // Retrieve chip clusters from resources
+        $chip_clusters = $this->resources->get_chip_clusters();
+
+        // Iterate over each cluster in the DataFrame
+        foreach ($df->indexValues() as $cluster) {
+            // Filter chip clusters based on the current cluster
+            $cluster_snps = $chip_clusters->filter(function ($row) use ($cluster) {
+                return strpos($row["clusters"], $cluster) !== false;
+            })->select(["chrom", "pos"]);
+
+            // Update the DataFrame with the number of SNPs in the cluster and in common with the current object
+            $df->loc[$cluster]["snps_in_cluster"] = count($cluster_snps);
+            $df->loc[$cluster]["snps_in_common"] = count($self_snps->merge($cluster_snps, "inner"));
+
+            // Calculate overlap ratios for cluster and self
+            $df["overlap_with_cluster"] = $df["snps_in_common"] / $df["snps_in_cluster"];
+            $df["overlap_with_self"] = $df["snps_in_common"] / count($self_snps);
+
+            // Find the cluster with the maximum overlap
+            $max_overlap = array_keys($df["overlap_with_cluster"], max($df["overlap_with_cluster"]))[0];
+
+            // Check if the maximum overlap exceeds the threshold for both cluster and self
+            if (
+                $df["overlap_with_cluster"][$max_overlap] > $cluster_overlap_threshold &&
+                $df["overlap_with_self"][$max_overlap] > $cluster_overlap_threshold
+            ) {
+                // Update the current object's cluster and chip based on the maximum overlap
+                $this->cluster = $max_overlap;
+                $this->chip = $df["chip_base_deduced"][$max_overlap];
+
+                $company_composition = $df["company_composition"][$max_overlap];
+
+                // Check if the current object's source is present in the company composition
+                if (strpos($company_composition, $this->source) !== false) {
+                    if ($this->source === "23andMe" || $this->source === "AncestryDNA") {
+                        // Extract the chip version from the company composition
+                        $i = strpos($company_composition, "v");
+                        $this->chip_version = substr($company_composition, $i, $i + 2);
+                    }
+                } else {
+                    // Log a warning about the SNPs data source not found
+                }
+            }
+        }
+
+        // Return the computed cluster overlap DataFrame
+        return $df;
+    }