d4:analyzefit {BCBCSF}

Functions for analyzing and visualizing a BCBCSF fitting result

Description

These functions are used to look at the fitting results, especially plot the gene signals.

Usage

reload_fit_bcbcsf (fit_bcbcsf_afile)

bcbcsf_sumfit (fit_bcbcsf = NULL, fit_bcbcsf_afile = NULL, 
               burn = NULL,  thin = 1)

bcbcsf_plotsumfit (sum_fit)
 

Arguments

fit_bcbcsf_afile

a string of name of a file saving a Markov chain fitting result; it can be found from the value fitfiles of function bcbcsf_fitpred.

fit_bcbcsf

a list of Markov chain fitting result, returned by function reload_fit_bcbcsf and bcbcsf_fitpred; if it is NULL, it will be retrieved by running reload_fit_bcbcsf with value in fit_bcbcsf_afile.

burn, thin

burn of Markov chain (super)iterations will be discarded (burned) for evaluation, and only every thinth are used; by default, 20% of (super)iterations are burned, and thin=1.

sum_fit

a list returned by function bcbcsf_sumfit

Value

reload_fit_bcbcsf returns a list of Markov chain fitting results, including how to do feature selection and data preprocessing.

bcbcsf_sumfit returns a list of point estimates of means and variances.

bcbcsf_plotsumfit returns nothing; it plots the normalized means (for each gene, original expression means substracted by their means and divided by the common standard deviation), and overall signals (Euclid distance of normalized means) for the selected features.