fit_powerest

This function loads the power values with corresponding avg_log2FC and avg_PCT derived from bootstrap sampling
and utilizes the <a href="https://CRAN.R-project.org/package=scam">scam</a> package to fit two dimensional
smoothing splines under monotone constraints: 1.positive relationship between power and avg_log2FC;
2.positive relationship between power and avg_PCT. The values of avg_log2FC and avg_PCT can be either
from the averages of the bootstrap samples or from the original spatial transcriptomics data.

Power estimation and sample size calculation for 10X Visium Spatial Transcriptomics data to detect differential expressed genes between two conditions based on bootstrap resampling. See Shui et al. (2025) <doi:10.1371/journal.pcbi.1013293> for method details.

Lan Shui

PoweREST

A Bootstrap-Based Power Estimation Tool for Spatial
Transcriptomics

fit_powerest function

<dl><dt>power</dt>
<dd>The raw power values.</dd>
<dt>avg_log2FC</dt>
<dd>The corresponding log2FC values.</dd>
<dt>avg_PCT</dt>
<dd>The corresponding PCT values.</dd>
<dt>filter_zero</dt>
<dd>Whether the user would like to filter to remove the power values being 0, default=TRUE.</dd></dl>

Arguments

Lan Shui <a href="/link/lshui%40mdanderson.org?package=PoweREST&version=0.1.2" data-mini-rdoc="PoweREST::lshui@mdanderson.org">lshui@mdanderson.org</a>

Author

This function loads the power values with corresponding avg_log2FC and avg_PCT derived from bootstrap sampling
and utilizes the <a href='https://CRAN.R-project.org/package=scam'>scam</a> package to fit two dimensional
smoothing splines under monotone constraints: 1.positive relationship between power and avg_log2FC;
2.positive relationship between power and avg_PCT. The values of avg_log2FC and avg_PCT can be either
from the averages of the bootstrap samples or from the original spatial transcriptomics data.

Fit the power surface — fit_powerest

<dl>

<dt>power</dt>
<dd>The raw power values.</dd>


<dt>avg_log2FC</dt>
<dd>The corresponding log2FC values.</dd>


<dt>avg_PCT</dt>
<dd>The corresponding PCT values.</dd>


<dt>filter_zero</dt>
<dd>Whether the user would like to filter to remove the power values being 0, default=TRUE.</dd>

</dl>

Lan Shui <a href='mailto:lshui@mdanderson.org'>lshui@mdanderson.org</a>

fit_powerest: Fit the power surface

Description

Usage

Value

Arguments

Author

Examples