This function is directly modified from the original irwsva.build() in the SVA package. It was noticed that under certain circumstances a subscript out of bounds error would occur while running the SVA function. Therefore, this modified code has a single line altered that conditionally uses the generic singular decomposition, svd(), instead of fast singular decomposition, fast.svd().
A screening process to filter out non-informative DNA methylation sites by applying (ordinary or robust) linear regressions to training data, and the results are further examined using testing samples. Surrogate variables are included to account for unknown factors.
A screening process to filter out non-informative DNA methylation sites by applying (ordinary or robust) linear regressions to training data, and the results are further examined using testing samples. Surrogate variables are included to account for unknown factors.
This function is directly modified from the orginal num.sv() in the sva package. This function has the tolerance level in the fast.svd() function set back to its orginal default instead of 0.
This function is the modified SVA function in which it uses the irwsva.build2 function rather than the irwsva.build function to build the surrogate variables. Thus, only a single line has been altered from the original SVA() function.
providing 
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