Closed star0044 closed 9 months ago
Hi, I didn't see any thing wrong in your script. It is possible that the correction didn't have any effect on the logR, which highly depends on your specific data. However, in your case, I can tell there is slightly changes before and after correction. You can check using the command ascat.metrics ((https://github.com/VanLoo-lab/ascat/blob/master/ASCAT/R/ascat.metrics.R)) for details. I also suggested that you discard the Y chromosome, but keep autosomes and X. Thanks a lot.
Thanks for the feedback. I removed the Y chromosome and re-ran the data. You were right, there are some slight differences, but nothing major.
Hello Van Loo lab. First off, thanks for developing and maintaining ASCAT. Your group recently added the Infinium GDAC + 8 platform for me, which was extremely helpful. I generated a GCContentFile using the SNP positions on this platform and the HG38 genome build using your R script and it appears to have worked. I then ran ASCAT on a set of 80 samples that we have run on the Infinium GDAC platform and plotted the LogR and BAF png images both before and after running the ascat.correctLogR function. When I look at the before and after images they look exactly the same. I don't think I messed up on the code, but maybe I am making some simple mistake.
Below is the code I used and then an example from one of the samples
Here is the code (note, I changed the ascat object from ascat.bc to ascat.ac after correction)
Create ASCAT object
ascat.bc = ascat.loadData(Tumor_LogR_file = paste0(infinium_data_input_directory, "logr_table.txt"), Tumor_BAF_file = paste0(infinium_data_input_directory, "baf_table.txt"), gender = rep('XX',100), genomeVersion = "hg38")
Plot the before correction data
ascat.plotRawData(ascat.bc, img.dir = paste0(cnv_output_directory), img.prefix = "Beforecorrection")
Use GC file to correct Logr
ascat.ac = ascat.correctLogR(ascat.bc, GCcontentfile = paste0(infinium_data_input_directory, "GCcontent_SNPloci.txt"))
Plot the after correction data
ascat.plotRawData(ascat.ac, img.dir = paste0(cnv_output_directory), img.prefix = "Aftercorrection")
Predict the before correction germline genotype
ascat.predictGermlineGenotypes(ascat.bc, platform = "IlluminaGDACyto-8", img.dir = cnv_output_directory, img.prefix = "predict_germlinebc")
Predict the after correction germline genotype
ascat.predictGermlineGenotypes(ascat.ac, platform = "IlluminaGDACyto-8", img.dir = cnv_output_directory, img.prefix = "predict_germlineac")
Here are the images produced LogR and BAF png before correction![Before_correction_PM_6_59 tumour](https://github.com/VanLoo-lab/ascat/assets/7323140/cefc45e5-8c30-4bd7-bd41-2617ecdef3a6)
LogR and BAF png after correction![After_correction_PM_6_59 tumour](https://github.com/VanLoo-lab/ascat/assets/7323140/27ede208-31f8-4ffa-a75b-c6a123e92f77)
Predict Germline png file before correction![predict_germline_bc_tumorSepPM_6_59](https://github.com/VanLoo-lab/ascat/assets/7323140/3032c5ef-d575-4a39-83b1-164e9ae56a28)
Predict Germline png after correction![predict_germline_ac_tumorSepPM_6_59](https://github.com/VanLoo-lab/ascat/assets/7323140/ecfe897a-f7f6-4324-9a72-6edb1d9e35c7)
And here is the head of the GCContent file Chr Position 25bp 50bp 100bp 200bp 500bp 1kb 2kb 5kb 10kb 20kb 50kb 100kb 200kb 500kb 1Mb 1:10001102-G-T 1 9941044 0.32 0.372549 0.376238 0.393035 0.379242 0.40959 0.453773 0.465107 0.460354 0.453527 0.450771 0.465335 0.483703 0.471763 0.471155 1:100011159-T-G 1 99545603 0.32 0.313725 0.356436 0.373134 0.345309 0.347652 0.370815 0.367526 0.371363 0.372581 0.365573 0.378886 0.378728 0.376799 0.376792 1:10002775-GA 1 9942717 0.24 0.372549 0.386139 0.422886 0.461078 0.462537 0.506747 0.480504 0.455754 0.450477 0.450591 0.464425 0.483093 0.471717 0.471038 1:100122796-C-T 1 99657240 0.4 0.431373 0.415842 0.41791 0.421158 0.403596 0.396802 0.368726 0.373563 0.365582 0.376892 0.383266 0.378803 0.381595 0.376948 1:100152282-CT 1 99686726 0.48 0.372549 0.39604 0.353234 0.327345 0.2997 0.348326 0.381724 0.384262 0.386831 0.381192 0.378646 0.382743 0.381421 0.377048
Any advice/help you can give is appreciated. Is it possible that the correction worked and there were no changes?
-Tim STarr