get_lsmeans

Compute the least squares means from a prediction grid and estimated coefficients

Provides functionality for quality control processing and statistical analysis of mass spectrometry (MS) omics data, in particular proteomic (either at the peptide or the protein level), lipidomic, and metabolomic data, as well as RNA-seq based count data and nuclear magnetic resonance (NMR) data. This includes data transformation, specification of groups that are to be compared against each other, filtering of features and/or samples, data normalization, data summarization (correlation, PCA), and statistical comparisons between defined groups. Implements methods described in: Webb-Robertson et al. (2014) <doi:10.1074/mcp.M113.030932>. Webb-Robertson et al. (2011) <doi:10.1002/pmic.201100078>. Matzke et al. (2011) <doi:10.1093/bioinformatics/btr479>. Matzke et al. (2013) <doi:10.1002/pmic.201200269>. Polpitiya et al. (2008) <doi:10.1093/bioinformatics/btn217>. Webb-Robertson et al. (2010) <doi:10.1021/pr1005247>.

Lisa Bramer

pmartR

Panomics Marketplace - Quality Control and Statistical Analysis
for Panomics Data

Kelly Stratton

Daniel Claborne

Evan Glasscock

Rachel Richardson

David Degnan

Evan Martin

get_lsmeans function

<dl><dt>data</dt>
<dd>The raw data from which the estimates were computed</dd>
<dt>xmatrix</dt>
<dd>The design matrix from which the prediction grid was constructed</dd>
<dt>pred_grid</dt>
<dd>The prediction grid, obtained from <code>get_pred_grid</code></dd>
<dt>Betas</dt>
<dd>The estimated coefficients</dd>
<dt>continuous_covar_inds</dt>
<dd>The column indices of xmatrix corresponding to continuous covariates.</dd></dl>

Arguments

Author

Compute the least squares means from a prediction grid and estimated coefficients — get_lsmeans

<dl>

<dt>data</dt>
<dd>The raw data from which the estimates were computed</dd>


<dt>xmatrix</dt>
<dd>The design matrix from which the prediction grid was constructed</dd>


<dt>pred_grid</dt>
<dd>The prediction grid, obtained from <code>get_pred_grid</code></dd>


<dt>Betas</dt>
<dd>The estimated coefficients</dd>


<dt>continuous_covar_inds</dt>
<dd>The column indices of xmatrix corresponding to continuous covariates.</dd>

</dl>

get_lsmeans: Compute the least squares means from a prediction grid and estimated coefficients

Description

Usage

Value

Arguments

Author