import_count_data

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

import_count_data function

<dl><dt>exp_design</dt>
<dd>Experimental design</dd>
<dt>t2g</dt>
<dd>Transcript to gene mapping</dd>
<dt>import_type</dt>
<dd>Import type</dd>
<dt>gene_level</dt>
<dd>Whether to aggregate to gene level</dd>
<dt>bootstrap</dt>
<dd>Whether to use bootstrap samples</dd></dl>

Arguments

Import count data from files — import_count_data

<dl>

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


<dt>t2g</dt>
<dd>Transcript to gene mapping</dd>


<dt>import_type</dt>
<dd>Import type</dd>


<dt>gene_level</dt>
<dd>Whether to aggregate to gene level</dd>


<dt>bootstrap</dt>
<dd>Whether to use bootstrap samples</dd>

</dl>

Import count data from files

import_count_data: Import count data from files

Description

Usage

Value

Arguments