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molgenis / NIPTeR

R Package for Non Invasive Prenatal Testing (NIPT) analysis
GNU Lesser General Public License v3.0
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GC_correct error #20

Closed missaileen closed 4 years ago

missaileen commented 4 years ago

I am new to NIPTeR and just working through the flow as per the Additional File 1 document of the paper. All seemed to be going smoothly until I got to the gc correction of the control group. I am getting the following error:

bingc_control_group <- gc_correct(nipt_object = NIPT_control_group_separate, method = "bin") Error in if (sum(reads != 0)) { : argument is not interpretable as logical

Would you have any suggestions on how to get around this?

Thanking you for your time,

ljohansson commented 4 years ago

This seems to be the same issue as: https://github.com/molgenis/NIPTeR/issues/18 Are you getting the error in the example data or in data procuced from bam files in other sampels? Does the LOESS GC correction also give such an error?

missaileen commented 4 years ago

I was getting the error using my own data for both LOESS and bin methods. In the end it was my mistake- i did not set the ref-genome parameter to hg38, once this was done the issue resolved and I was able to proceed. Thank you

ljohansson commented 4 years ago

Good to hear. Thanks for letting is know.

Hafsah35 commented 1 year ago

Hallo, I got the same issue with @missaileen and I changed the reference genome to hg38, but I got a new issue

sample_of_interest <- gc_correct(nipt_object = sample_of_interest, method = "bin") Error in gc_correct(nipt_object = sample_of_interest, method = "bin") : object 'NIPT_sample_class' not found

what should I do to fix this thing? @ljohansson