convert_to_long_format

Convert count matrix to long format and join with experiment design

internal

Provides a comprehensive framework for time series omics analysis,
integrating changepoint detection, smooth and shape-constrained trends,
and uncertainty quantification. It supports gene- and transcript-level inferences,
p-value aggregation for improved power, and both case-only and case-control designs.
It includes an interactive 'shiny' interface. The methods are described in Yates et al. (2024) <doi:10.1101/2024.12.22.630003>.

Luke Yates

cpam

Changepoint Additive Models for Time Series Omics Data

Michael Charleston

Jazmine Humphreys

Steven Smith

convert_to_long_format function

<dl><dt>counts_raw</dt>
<dd>Raw count matrix</dd>
<dt>exp_design</dt>
<dd>Experimental design</dd></dl>

Arguments

Convert count matrix to long format and join with experiment design — convert_to_long_format

<dl>

<dt>counts_raw</dt>
<dd>Raw count matrix</dd>


<dt>exp_design</dt>
<dd>Experimental design</dd>

</dl>

convert_to_long_format: Convert count matrix to long format and join with experiment design

Description

Usage

Value

Arguments