surv_designation

This function will add the necessary information to omicsData such that
survival analysis can be applied to it.

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

surv_designation function

<dl><dt>omicsData</dt>
<dd>an object of the class 'lipidData', 'metabData', 'pepData',
or 'proData' usually created by <code>as.lipidData</code>,
<code>as.metabData</code>, <code>as.pepData</code>, or
<code>as.proData</code>, respectively.</dd>
<dt>t_death</dt>
<dd>the column in 'f_data' that corresponds to the subjects' time
of death</dd>
<dt>t_progress</dt>
<dd>the column in 'f_data' that corresponds to the subjects'
time of progression</dd>
<dt>ind_death</dt>
<dd>the column in 'f_data' that corresponds to the subjects'
status, e.g. alive/dead</dd>
<dt>ind_progress</dt>
<dd>the column in 'f_data' that corresponds to the subjects'
progression status</dd>
<dt>covariates</dt>
<dd>the column(s) in 'f_data' that correspond to covariates to
be included in the survivial analysis</dd></dl>

Arguments

Author

Create a "surv_DF" attribute so that survival analysis can be implemented. — surv_designation

<dl>

<dt>omicsData</dt>
<dd>an object of the class 'lipidData', 'metabData', 'pepData',
or 'proData' usually created by <code>as.lipidData</code>,
<code>as.metabData</code>, <code>as.pepData</code>, or
<code>as.proData</code>, respectively.</dd>


<dt>t_death</dt>
<dd>the column in 'f_data' that corresponds to the subjects' time
of death</dd>


<dt>t_progress</dt>
<dd>the column in 'f_data' that corresponds to the subjects'
time of progression</dd>


<dt>ind_death</dt>
<dd>the column in 'f_data' that corresponds to the subjects'
status, e.g. alive/dead</dd>


<dt>ind_progress</dt>
<dd>the column in 'f_data' that corresponds to the subjects'
progression status</dd>


<dt>covariates</dt>
<dd>the column(s) in 'f_data' that correspond to covariates to
be included in the survivial analysis</dd>

</dl>

surv_designation: Create a "surv_DF" attribute so that survival analysis can be implemented.

Description

Usage

Value

Arguments

Author