bapred

Various tools dealing with batch effects, in particular enabling the removal of discrepancies between training and test sets in prediction scenarios. Moreover, addon quantile normalization and addon RMA normalization (Kostka & Spang, 2008) is implemented to enable integrating the quantile normalization step into prediction rules. The following batch effect removal methods are implemented: FAbatch, ComBat, (f)SVA, mean-centering, standardization, Ratio-A and Ratio-G. For each of these we provide an additional function which enables a posteriori ('addon') batch effect removal in independent batches ('test data'). Here, the (already batch effect adjusted) training data is not altered. For evaluating the success of batch effect adjustment several metrics are provided. Moreover, the package implements a plot for the visualization of batch effects using principal component analysis. The main functions of the package for batch effect adjustment are ba() and baaddon() which enable batch effect removal and addon batch effect removal, respectively, with one of the seven methods mentioned above. Another important function here is bametric() which is a wrapper function for all implemented methods for evaluating the success of batch effect removal. For (addon) quantile normalization and (addon) RMA normalization the functions qunormtrain(), qunormaddon(), rmatrain() and rmaaddon() can be used.

Last 30 days

This package has been downloaded 270 times in the last 30 days. Enough downloads to make a small wave in the niche community. The curiosity is spreading! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 11 times.

The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.

Last 365 days

This package has been downloaded 3,273 times in the last 365 days. Consider this 'mid-tier influencer' status—if it were a TikTok, it would get a nod from nieces and nephews. The day with the most downloads was May 08, 2024 with 37 downloads.

The following line graph shows the downloads per day. You can hover over the graph to see the exact number of downloads per day.