--maxThreshold only affects heatmaps put not profiles.

[dpryan79]

Realistically, the profile should be an accurate summarization of the underlying matrix and heatmap. So if we exclude rows from the heatmaps due to --maxThreshold or --minThreshold then they should be excluded from the profiles as well. These should also not affect things like cluster, so we might as well filter rows immediately after loading the matrix so every other step will definitely fit. The only difficulty to this will be ensuring the group bounds are maintained. I think the proper implementation will be some sort of valueFilter function in computeMatrixOperations with min and max options. The matrix load function can then simply call that.

[dpryan79]

This is now in develop.