Dynamic_Window_SCANG error(s)

xihaoli / STAARpipeline-Tutorial

The tutorial for performing single-/multi-trait association analysis of whole-genome/whole-exome sequencing (WGS/WES) studies using FAVORannotator, STAARpipeline and STAARpipelineSummary

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Dynamic_Window_SCANG error(s) #40

Closed lj1257111 closed 6 months ago

lj1257111 commented 8 months ago

Hello, I have been receiving two errors.

Error 1 occurs when "res" (a SCANG output) all equal zero, or not applicable, the pipeline breaks before moving to next sub_seq_num. This is usually fixed by increasing the rare_maf_cutoff value.

Error 2 I am not sure what is going on: Error in resmost_SCANG_O[1, 3] - resmost_SCANG_O[1, 2] : non-numeric argument to binary operator Calls: Dynamic_Window_SCANG -> matrix Execution halted

Appreciate any help! Thanks lj

zilinli1988 commented 8 months ago

What is your sample size?

lj1257111 commented 8 months ago

100 samples

zilinli1988 commented 8 months ago

SCANG is designed for moderate or large samples. When applying it to small samples, you should set the MAF cutoff at least 0.1.