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snp_list format #1

Open jmbeesley opened 5 years ago

jmbeesley commented 5 years ago

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

rleylek commented 4 years ago

Hi, I have the same question, did anyone solve this? Thanks! -Rebecca

jmbeesley commented 4 years ago

Hi Rebecca

This format worked:

rs3007733   chr1    18800911
rs1360915   chr1    18801804
rs1316327   chr1    18802387
rs2992732   chr1    18802825
rs3007734   chr1    18803022

JB

Sophiesze commented 3 years ago

@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