NeoLoopFinder for Micro-C

[PinpinSui]

Hi Xiaotao,

Thank you very much for this wonderful tool. Does NeoLoopFinder apply to MicroC data? And "uniform" should be selected for "-e" parameter?
Thank you,

Pinpin

[PinpinSui]

Hi Xiaotiao,
When I use -e uniform for 500M Micro-C contactmatrix, The following error occurred. What is the possible reason?
The commond is as follows: calculate-cnv(0.4.3-r2) -H matrix.mcool::resolutions/16000 -g hg38 -e uniform --output mc_16kb.CNV-profile.bedGraph
Thank you,
Pinpin

[XiaoTaoWang]

Hi Pinpin, this seems just a warning message, did you get any results in the end?

[PinpinSui]

Hi Xiaotao,

Just a log file genarated: cnv-calculation.log and no other output. The content within the log file is as follows.

rpy2.rinterface_lib.embedded INFO @ 04/03/23 08:03:08: Default options to initialize R: rpy2, --quiet, --no-save
rpy2.rinterface_lib.embedded INFO @ 04/03/23 08:03:09: R is already initialized. No need to initialize.
root INFO @ 04/03/23 08:03:11: Calculate the 1D coverage from Hi-C matrix ...
root INFO @ 04/03/23 08:03:26: Load GC content ...
root INFO @ 04/03/23 08:04:08: Load mappability scores ...
root INFO @ 04/03/23 08:04:50: Count the number of cut sizes for each bin ...
root INFO @ 04/03/23 08:05:23: Filter out invalid bins ...
root INFO @ 04/03/23 08:05:23: Done
root INFO @ 04/03/23 08:05:23: Fitting a Generalized Additive Model with log link and Poisson distribution ...
rpy2.rinterface_lib.callbacks WARNING @ 04/03/23 08:05:29: R[write to console]: Error in smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) :
A term has fewer unique covariate combinations than specified maximum degrees of freedom

Traceback (most recent call last):
File "/data/suip/software/anaconda3/envs/neoloop/bin/calculate-cnv", line 164, in run
gam = mgcv.gam(fomula, family=stats.poisson(link='log'))
File "/data/suip/software/anaconda3/envs/neoloop/lib/python3.10/site-packages/rpy2/robjects/functions.py", line 208, in call
return (super(SignatureTranslatedFunction, self)
File "/data/suip/software/anaconda3/envs/neoloop/lib/python3.10/site-packages/rpy2/robjects/functions.py", line 131, in call
res = super(Function, self).call(*new_args, **new_kwargs)
File "/data/suip/software/anaconda3/envs/neoloop/lib/python3.10/site-packages/rpy2/rinterface_lib/conversion.py", line 45, in _
cdata = function(*args, **kwargs)
File "/data/suip/software/anaconda3/envs/neoloop/lib/python3.10/site-packages/rpy2/rinterface.py", line 817, in call
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in smooth.construct.tp.smooth.spec(object, dk$data, dk$knots) :
A term has fewer unique covariate combinations than specified maximum degrees of freedom

When I use higher 32kb resolution, I can be run successfully.

Thank you,
Pinpin

[iagooteroc]

Hello. This also happens to me with 25kb resolution and -e uniform

calculate-cnv -H Micro-C_H2087_E0016_balanced.mcool::resolutions/25000 \
-g hg38 -e uniform --output Micro-C_H2087_E0016_25k.CNV-profile.bedGraph

As @PinpinSui said, with a higher binsize (50kb in my case) it worked.