Last updated: 2023-11-13

Checks: 1 1

Knit directory: multigroup_ctwas_analysis/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

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Repository version: 909f2ad

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The results in this page were generated with repository version 909f2ad. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Untracked files:
    Untracked:  analysis/data.Rmd

Unstaged changes:
    Modified:   analysis/index.Rmd
    Modified:   analysis/multi_tissue.Rmd

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GWAS

Sample size Ancestry ID Year ref link
IBD (same with ctwas paper) 59,957 Mixed ebi-a-GCST004131 2017 PMID: 28067908 https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST004131/
SBP (same with ctwas paper) 317,754 European ukb-a-360 2017 Rapid GWAS Project. In: http://www.nealelab.is/uk-biobank (accessed in 2021). https://gwas.mrcieu.ac.uk/datasets/ukb-a-360/
LDL (same with ctwas paper) 343,621 European ukb-d-30780_irnt 2018 same with above https://gwas.mrcieu.ac.uk/datasets/ukb-d-30780_irnt/
SCZ 127,906 European ieu-b-5102 2022 PMID: 35396580 https://gwas.mrcieu.ac.uk/datasets/ieu-b-5102/
AFib 1,030,836 European ebi-a-GCST006414 2018 PMID: 30061737 https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST006414/
Asthma 361,194 European ukb-d-J10_ASTHMA 2018 http://www.nealelab.is/uk-biobank/ (cite this website) https://gwas.mrcieu.ac.uk/datasets/ukb-d-J10_ASTHMA/
WBC 563,946 European ieu-b-30 2020 PMID: 32888494 https://gwas.mrcieu.ac.uk/datasets/ieu-b-30/

Weights

PredictDB weights

storaged in /project2/xinhe/shared_data/multigroup_ctwas/weights/predictdb_nolnc/mashr_“$WEIGHT”_nolnc.db

LD ref

from UKBB

storaged in

hg38 /project2/mstephens/wcrouse/UKB_LDR_0.1/

hg37 /project2/mstephens/wcrouse/UKB_LDR_0.1_b37/

download: https://uchicago.box.com/s/jqocacd2fulskmhoqnasrknbt59x3xkn