| confounders_lsq_barchart {structToolbox} | R Documentation |
A barchart of the relative change (delta) in regression coefficient when potential confounding factors are included, and excluded, from the model. Factors with a large delta are considered to be confounding factors.
confounders_lsq_barchart(feature_to_plot, threshold = 10, ...)
feature_to_plot |
(numeric, character, integer) The column name of the feature to be plotted. |
threshold |
(numeric) A horizontal line is plotted to indicate the threshold. The default is |
... |
Additional slots and values passed to |
A confounders_lsq_barchart object.
D = MTBLS79_DatasetExperiment()
M = filter_by_name(mode='include',dimension='variable',
names=colnames(D$data)[1:10]) + # first 10 features
filter_smeta(mode='exclude',levels='QC',
factor_name='class') + # reduce to two group comparison
confounders_clsq(factor_name = 'class',
confounding_factors=c('sample_order','batch'))
M = model_apply(M,D)
C = C=confounders_lsq_barchart(feature_to_plot=1,threshold=15)
chart_plot(C,M[3])