extract_ranked

rankEN_obj

Either <code>TRUE</code> or <code>FALSE</code>, specifying whether a
column should be included in the returning <code>data.frame</code> providing
the correlation between the compound and the within-fraction average of
the bioactivity replicates in the region of interest.

include_cor


Extract an ordered list of candidate compounds from a <code>rankEN</code> object.
The list is presented in the form of a <code>data.frame</code>, such that each row
provides the identifying information for a particular candidate compound, and
with the rows arranged in the order that the compounds entered the elastic
net model (i.e. row 1 is the earliest, row 2 the 2nd earliest, etc.).  The
columns of the <code>data.frame</code> provide the mass-to-charge information,
charge information, and possibly the correlation between the compound and the
within-fraction average of the bioactivity replicates in the region of
interest.


An implementation of the data processing and data analysis portion
of a pipeline named the PepSAVI-MS which is currently under development by
the Hicks laboratory at the University of North Carolina.  The statistical
analysis package presented herein provides a collection of software tools
used to facilitate the prioritization of putative bioactive peptides from a
complex biological matrix.  Tools are provided to deconvolute mass
spectrometry features into a single representation for each peptide charge
state, filter compounds to include only those possibly contributing to the
observed bioactivity, and prioritize these remaining compounds for those
most likely contributing to each bioactivity data set.

extract_ranked: Extract candidate compounds

Description

Usage

Arguments