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ramiromagno / gwasrapidd

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
https://rmagno.eu/gwasrapidd/
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How download TSV file like on the web GWAS Catalog？or any function can do like that？ #47

Closed sher-l closed 1 month ago

sher-l commented 7 months ago

how can I get those? ‘ variant_id p_value chromosome base_pair_location effect_allele other_allele effect_allele_frequency odds_ratio ci_lower ci_upper
rs888953847 0.9626 1 594445 T C 6e-04 0.985 0.522 1.857 -0.0152 0.3236 20301 21839 0 1 chr1:594445:C:T rs1040232850 0.267 1 595762 CTG C 0.9986 0.779 0.502 1.210 -0.2494 0.2247 26798 28624 0 0.528 chr1:595762:CTG:C rs1390538076 0.8214 1 630947 A G 3e-04 1.102 0.473 2.571 0.0975 0.432 20301 21839 0 1 chr1:630947:G:A ... ’ Thanks.

ramiromagno commented 7 months ago

Hello @sher-l ,

Thank you for reaching out.

To help you, can you tell what is the query behind those associations? If by study identifier, then look at: https://github.com/ramiromagno/gwasrapidd/issues/31.

sher-l commented 7 months ago

Hello @sher-l ,

Thank you for reaching out.

To help you, can you tell what is the query behind those associations? If by study identifier, then look at: #31.

Actually, I need to perform Mendelian randomization analysis using TwoSampleMR, so I need the gwas dataset. Can I get content that can be used for TwoSampleMR through gwasrapidd?

Thank a lot.

ramiromagno commented 7 months ago

I am not familiarized with the data needed for the R package TwoSampleMR.

For me to write R code that will generate the table you posted above, could you please share a motivating query so that I can create a self-contained example?

sher-l commented 7 months ago

https://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90091001-GCST90092000/GCST90091033/GCST90091033_buildGRCh37.tsv.gz

ramiromagno commented 7 months ago

Hi @sher-l,

From your messages, I get the feeling you need help on a level beyond the objective usage of gwasrapidd. So the questions raised in this issue might be out of scope. I am happy to help nonetheless --- feel free to contact me by email (my email can be found in this file https://github.com/ramiromagno/gwasrapidd/blob/master/DESCRIPTION).