validate_inputs

Validate input parameters for prepare_cpam

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

validate_inputs function

<dl><dt>exp_design</dt>
<dd>Experimental design data frame</dd>
<dt>count_matrix</dt>
<dd>Count matrix</dd>
<dt>t2g</dt>
<dd>Transcript to gene mapping</dd>
<dt>import_type</dt>
<dd>Import type</dd>
<dt>model_type</dt>
<dd>Model type</dd>
<dt>condition_var</dt>
<dd>Condition variable</dd>
<dt>case_value</dt>
<dd>Case value</dd>
<dt>fixed_effects</dt>
<dd>Fixed effects formula</dd>
<dt>aggregate_to_gene</dt>
<dd>Whether to aggregate to gene level</dd>
<dt>gene_level</dt>
<dd>Whether data is at gene level</dd>
<dt>import</dt>
<dd>Whether to import data</dd></dl>

Arguments

Validate input parameters for prepare_cpam — validate_inputs

<dl>

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


<dt>count_matrix</dt>
<dd>Count matrix</dd>


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


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


<dt>model_type</dt>
<dd>Model type</dd>


<dt>condition_var</dt>
<dd>Condition variable</dd>


<dt>case_value</dt>
<dd>Case value</dd>


<dt>fixed_effects</dt>
<dd>Fixed effects formula</dd>


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


<dt>gene_level</dt>
<dd>Whether data is at gene level</dd>


<dt>import</dt>
<dd>Whether to import data</dd>

</dl>

validate_inputs: Validate input parameters for prepare_cpam

Description

Usage

Value

Arguments