The qsip_data object holds validated qSIP source, sample and feature metadata,
and has slots to store all of the subsequence qSIP2 analysis.
Details
qsip_data() is not a typical function, but rather a class constructor that
instantiates a new qsip_data object. The constructor takes a qsip_source_data,
qsip_sample_data and qsip_feature_data as input and returns a validated qsip_data
object.
This qsip_data object holds the source, sample and feature data. It also creates empty
slots to hold the filtering results, the resampling and the EAF values from their
associated functions. For this reason, the qsip_data object is intended to be
progressively overwritten with new analysis results, but new objects can be created
at any point in the analysis, if necessary. For example, a study with multiple comparison
groups might be combined into one large qSIP_data object, and then split into separate
objects at the run_feature_filtering() step.
Internally, creating the original qSIP objects renames the metadata columns to be standardized
to MISIP terminology. A data.frame with the standardized names can be extracted
back out of the qSIP_data using the get_dataframe() method and a required type argument
of "source", "sample" or "feature". The optional original_headers
argument can be set to TRUE to return the original column names.
See also
Other "qSIP Objects":
qsip_feature_data(),
qsip_sample_data(),
qsip_source_data()