GenerateInput

Generate pattern level data for cell type annotation

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

GenerateInput function

<dl><dt>query_fn</dt>
<dd>File path to query .cg</dd>
<dt>knowledge_fn</dt>
<dd>File path to pattern file .cm</dd></dl>

Arguments

Generate pattern level data for cell type annotation — GenerateInput

<dl>

<dt>query_fn</dt>
<dd>File path to query .cg</dd>


<dt>knowledge_fn</dt>
<dd>File path to pattern file .cm</dd>

</dl>

GenerateInput: Generate pattern level data for cell type annotation

Description

Usage

Value

Arguments

Examples