ChAMP filter bug when using beta matrix and pd as input
1
0
Entering edit mode
@allenyuchishing-13300
Last seen 7.4 years ago

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.

ChAMP • 1.6k views
ADD COMMENT
0
Entering edit mode
Yuan Tian ▴ 90
@yuan-tian-9598
Last seen 4.8 years ago

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

 

ADD COMMENT
0
Entering edit mode

Thank you very much for the quick fix! 

ADD REPLY

Login before adding your answer.

Traffic: 811 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6