When I supply beta matrix and pd directly to champ.filter using the following function call:

champ.filter(beta=beta, pd=pd, autoimpute = F, filterDetP = F, filterBeads = F,  arraytype = "EPIC")

The following error would appear:

Updating PD file
Error in `[.data.frame`(pd, RemainSample, ) : 
  object 'RemainSample' not found

In the source code of champ.filter.R, line 324:

pd <- pd[RemainSample,]

The variable RemainSample would be uninitialized, if FilterOption$filterDetP == FALSE, thus causing the error.

Hello:

Yes it's obviously a small bug in champ.filter(). Thanks very much to spot it. I have fixed this bug in current version (2.8.3) ChAMP, it should be online in 24 or 36 hours. I forget that RemainSample is the variable I declared in filterDetP if block.

my fix message should be appear on below link soon.

https://www.bioconductor.org/packages/release/bioc/news/ChAMP/NEWS

Sorry for the bug and thanks for the help.^_^

Best

Yuan Tian