Merge pull request #1306 from SamuelSun2000/main

initial_scaling

Author: gaow

code/reference_data/rss_ld_sketch.ipynb

@@ -638,6 +638,14 @@
     "    G = np.array(dosage_matrix, dtype=np.float32).T  # (n_samples, n_variants)\n",
     "    del dosage_matrix\n",
     "    G = fill_missing_col_means(G)\n",
+    "\n",
+    "    # variant-wise scaling\n",
+    "    col_mean = G.mean(axis=0, keepdims=True)\n",
+    "    col_std  = G.std(axis=0, keepdims=True)\n",
+    "    # avoid division by zero\n",
+    "    col_std[col_std == 0] = 1.0\n",
+    "    G = (G - col_mean) / col_std\n",
+    "\n",
     "    U = W.T @ G  # (B, n_variants)\n",
     "    del G\n",
     "\n",
@@ -806,6 +814,7 @@
   },
   {
    "cell_type": "markdown",
+   "id": "1968fbf4",
    "metadata": {},
    "source": [
     "### Step 4 -- Load LD sketch data into R\n",
@@ -822,7 +831,10 @@
   },
   {
    "cell_type": "code",
+   "execution_count": null,
+   "id": "8a05b576",
    "metadata": {},
+   "outputs": [],
    "source": [
     "library(pecotmr)\n",
     "\n",
@@ -843,12 +855,11 @@
     "})\n",
     "cat(\"R dimensions:\", dim(res_r$LD_matrix), \"\\n\")\n",
     "res_r$LD_matrix[1:3, 1:3]"
-   ],
-   "outputs": [],
-   "execution_count": null
+   ]
   },
   {
    "cell_type": "markdown",
+   "id": "aad6e458",
    "metadata": {},
    "source": [
     "**Tested output** (ADSP R5 EUR chr22, 10000 pseudo-samples, 2Mb region, 9188 variants):\n",
@@ -903,7 +914,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.13"
+   "version": "3.12.2"
   },
   "sos": {
    "kernels": [
@@ -920,4 +931,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}