Open jmbeesley opened 5 years ago
Hi, I have the same question, did anyone solve this? Thanks! -Rebecca
Hi Rebecca
This format worked:
rs3007733 chr1 18800911
rs1360915 chr1 18801804
rs1316327 chr1 18802387
rs2992732 chr1 18802825
rs3007734 chr1 18803022
JB
@jmbeesley Hi,
I am still confused about what kind of format should be the input data. Does this format come from GWAS summary statistics? The template format you show seems to be the first three-row of the summary statistics from GWAS.
I also look into the fine-mapping data (Farh KK-H, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJH, Shishkin AA, et al. (2015). Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337–343.). Would it be okay to only use the column: 'SNP', 'chr', 'pos' from different traits in the dataset? It will be very helpful!
Thank you so much for your help!
Best, Sophie
Hi
Just wondering about the format for the input snp_list? I have SNPs from a fine-mapping project that I'd like to test. Neither a 3 column, a 4 column BED file, with or without a header line seem to work.
Errors are either:
File "code/CHEERS-master/CHEERS_computeEnrichment.py", line 213, in
position = float(ldParts[2])
ValueError: could not convert string to float:
or
File "code/CHEERS-master/CHEERS_computeEnrichment.py", line 350, in
mean_sd = math.sqrt((N*2-1)/(12n))
ZeroDivisionError: integer division or modulo by zero
Thanks! Jonathan