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Merged
gaow merged 1 commit into from
Mar 30, 2026
Merged

initial_scaling #1306

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21 changes: 16 additions & 5 deletions code/reference_data/rss_ld_sketch.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -806,6 +814,7 @@
},
{
"cell_type": "markdown",
"id": "1968fbf4",
"metadata": {},
"source": [
"### Step 4 -- Load LD sketch data into R\n",
Expand All @@ -822,7 +831,10 @@
},
{
"cell_type": "code",
"execution_count": null,
"id": "8a05b576",
"metadata": {},
"outputs": [],
"source": [
"library(pecotmr)\n",
"\n",
Expand All @@ -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",
Expand Down Expand Up @@ -903,7 +914,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.12.13"
"version": "3.12.2"
},
"sos": {
"kernels": [
Expand All @@ -920,4 +931,4 @@
},
"nbformat": 4,
"nbformat_minor": 5
}
}