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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
GNU General Public License v3.0
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Error in Gene Centric Analysis #51

Closed GACGAMA closed 6 months ago

GACGAMA commented 6 months ago

Hi Xihao! This is related to #14

My cohort is considerably small, with ~60 samples When doing the gene centric analysis, I can divide the jobs in many different arrays, but this errors with these two:


Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff,  : 
  Number of rare variant in the set is less than 2!
Error in STAAR(Geno, obj_nullmodel, Anno.Int.PHRED.sub.category, rare_maf_cutoff = rare_maf_cutoff,  : 
  genotype is not a matrix!

My question is if it would be better to reduce the number of divisions in each array or if this is ok because each gene is analyzed separately anyways

xihaoli commented 6 months ago

Hi @GACGAMA,

Thanks for letting me know. As noted in #14, these messages are not errors from your scripts, but they serve as indications of certain functional categories of genes that do not have at least 2 rare variants to form a variant set.

It is okay to run the current gene-centric analysis, as each gene is analyzed separately indeed.

Best, Xihao