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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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How to get the variable genes_info in STAARpipeline_Gene_Centric_Coding.r #1

Closed hmutanqilong closed 2 years ago

hmutanqilong commented 2 years ago

Hi, I am trying to learn this STAAR pipeline to deal with rare variant analysis. However, when I ran the Gene_Centric_Coding script, I found that I did not have the genes_info as the input file. So, how to get the genes_info file.

###########################################################
#           Main Function 
###########################################################
## gene number in job
gene_num_in_array <- 50 
group.num.allchr <- ceiling(table(genes_info[,2])/gene_num_in_array)
sum(group.num.allchr)
hmutanqilong commented 2 years ago

OK, I have known if I load STAARpipeline, I will get the genes_info. Thanks!

xihaoli commented 2 years ago

Yes, genes_info is an object embedded in the STAARpipeline package. Please let me know if you have any other questions. Thanks!