Error logical subscript too long when training data

[KhanhLPBao]

I'm trying to train a new batch of data, after loading all .bed file the script show this error and stop

Error in training.frame.sub["X" == training.frame$chr, ] : 
  (subscript) logical subscript too long
Calls: train -> as.data.frame
Execution halted

Does anyone know how to fix it? Thank you very much

[leraman]

I'm guessing one or more of your bed files have an different number of lines per chromosome? Could you double check they were all created with the same WCX reference?

[KhanhLPBao]

Sorry for not reply for long time, I will check all files again. Thank you very much

[KhanhLPBao]

@leraman
I have rerun entire entire samples, check their lines and they are the same but the problem still occured. My procedure including:

1. Convert .bam to .npz by using WisecondorX
2. Make the .bed by WisecondorX predict, the reference is the total male sample I made with command:

WisecondorX newref /path/to/samples sampleM.npz --yfrac 0
(I set yfrac = 0 to set all samples are male)

3. Create .bed file that PREFACE can read by command

cut -f1,2,3,5 *_bins.bed > *.bed

[leraman]

You should use --nipt during WisecondorX newref if you want to create a NIPT reference.

[KhanhLPBao]

@leraman Hi
I have tried to use --nipt but its returned with this output:

A NIPT reference should have at least 5 female feti samples. Removing --nipt flag.

I know the Y chromosome depend on the fetal fraction on the sample, but is there any way can I do to calculate ff based on Y fraction? Because as I mentioned in issue #6 the results are just repeating of 2-3 numbers and the r is very low.

[leraman]

For NIPT, you cannot analyze the y chromosome with WisecondorX, so you'll need to use --nipt and don't use --yfrac. We haven't provided code to calculate FFY, but there are multiple possibilities. You'll have to do some custom parsing on the bam files to define an FFY that best fits your protocol.

[cverwimp]

I encountered the same error, fixed it by replacing line 191 of PREFACE.R with:

training.frame <- training.frame[training.frame$chr != 'Y', ]

[leraman]

Hi @cverwimp

Did you use WisecondorX (if yes: you should use the --nipt flag, which makes sure there is no Y data) or some other software for copy number profiling?

Thanks,

Lennart

[happenywong]

I'm trying to train a new batch of data, after loading all .bed file the script show this error and stop

Error in training.frame.sub["X" == training.frame$chr, ] : 
  (subscript) logical subscript too long
Calls: train -> as.data.frame
Execution halted

Does anyone know how to fix it? Thank you very much

I met the same problem, how did you solve it?

[happenywong]

I encountered the same error, fixed it by replacing line 191 of PREFACE.R with:

training.frame <- training.frame[training.frame$chr != 'Y', ]

I used your method to solve the problem，thank！