smooth_matrix

Smooth cell by pattern matrix to reduce noise

Methods for analyzing DNA methylation data via Most Recurrent Methylation Patterns (MRMPs). Supports cell-type annotation, spatial deconvolution, unsupervised clustering, and cancer cell-of-origin inference. Includes C-backed summaries for YAME “.cg/.cm” files (overlap counts, log2 odds ratios, beta/depth aggregation), an XGBoost classifier, NNLS deconvolution, and plotting utilities. Scales to large spatial and single-cell methylomes and is robust to extreme sparsity.

Hongxiang Fu

MethScope

Ultra-Fast Analysis of Sparse DNA Methylome via Recurrent
Pattern Encoding

Wanding Zhou

The SAMtools/HTSlib authors 

Attractive Chaos

smooth_matrix function

<dl><dt>predictMatrix</dt>
<dd>A wide cell by pattern matrix generated from GenerateInput function</dd>
<dt>KNeighbor</dt>
<dd>Number of knn neighbors to use for smoothing (Default: 5)</dd></dl>

Arguments

Smooth cell by pattern matrix to reduce noise — smooth_matrix

<dl>

<dt>predictMatrix</dt>
<dd>A wide cell by pattern matrix generated from GenerateInput function</dd>


<dt>KNeighbor</dt>
<dd>Number of knn neighbors to use for smoothing (Default: 5)</dd>

</dl>

smooth_matrix: Smooth cell by pattern matrix to reduce noise

Description

Usage

Value

Arguments