gusevlab / stratas Goto Github PK

Dear Dr. Gusev,

I am very interesting about stratAS.
However, I did not find any format guide to the input file for stratas.R.
Rscript stratas.R
--input $OUT.MAT.split.00
--samples SAMPLES.ID
--peaks gencode.protein_coding.transcripts.bed
--global_param GLOBAL.params
--local_param LOCAL.params \

I am wondering where I can find some guide or example for these input files?

Thank you!

Hi, it appears that the file "KIRC.gexp" in the example folder is incomplete as it contains only one row with sample IDs. To ensure the correct format, could you please provide an example of a complete total activity matrix file? This will help us understand the expected format accurately. Thank you so much!

Dear Dr. Gusev,
I am very interesting about stratAS.
And I tried to use my own data to do the calculation, but unfortunately, when I went to the last step (hoping to calculate the QTL through Stratas.r) , the results were not so good, only the column name output, not the value. As there is no error warning during this process, so I hope to have the honor of your guidance;
I ran the code as follows:
Rscript stratas.R --input ${OUT}/ten_test.MAT.split.00 --samples ${OUT}/SAMPLES.ID.txt --peaks ${OUT}/ten_peaks.bed --global_param ${OUT}/test_T.global.params > ${OUT}/ten.AI.txt
I also looked at my input file to see if it differed from your sample file. Except for the difference between the name of the chromosome and the name of the SNP, everything else is the same (e.g. I'm“1” instead of your“chr1” and“1:3435433” instead of your“rs3435433”)

Hi @sashagusev @cakalita

Thanks for the great software!

I want to learn DeCAF and make sure I run the DeCAF correctly.But startAS branch DeCAF's example data ,such as KIRC.ALL.AS.filtered_01A.vcf.gz KIRC.ALL.AS.filtered_01A.counts are not given.

Thanks in advanced!