In ericwatt/eapath: Computational Models for Estrogen and Androgen Receptor Activity

Workflow

Aqcuire data

Generate synthetic points

Run model

Differences between ER and AR models

The selection of the ER or AR model causes differences in the following functions and parameters

Flagged

• tmat_va(). Function that returns a matrix of AUC receptors to calculate and 0 or 1 values for which assays should be included in the given AUC calculation. Specifying pathway = "ER" or pathway = "AR" will cause a different matrix to be returned, corresponding to the specified model.
• nconc Formerly the global variable NCONC
• conclist Formerly the global variable CONCLIST
• nassay Formerly the global variable NASSAY
• nreceptor Formerly the global variable NRECEPTOR
• aucscale1 Formerly the global variable AUCSCALE1
• aucscale2 Formerly the global variable AUCSCALE2
• assay_order
• pseudo_receptor_columns
• auc_names
• modl_ga_cols
• modl_tp_cols
• modl_gw_cols
• alpha. Formerly the global variable ALPHA, this is 1 for the ER model and 0.05 for the AR model. Used in penalty() and now given as a parameter for penalty with default NULL, which gets set to 1 if the ER model or 0.05 if AR.

ericwatt/eapath documentation built on May 16, 2019, 8:41 a.m.