SMR

Summary-data-based Mendelian Randomization

Download

SMR software tool: executable files (version 0.68)

smr_Linux.zip

smr_Mac.zip

smr_Win.zip

The executable files (binary code) are released under MIT lincense.

Westra eQTL summary data (Westra et al. 2013 Nat Genet) in SMR binary (BESD) format

westra_eqtl_data_hg18.zip (hg18)

westra_eqtl_data_hg19.zip (hg19)

CAGE eQTL summary data (Luke R. Lloyd-Jones et al. 2017 AJHG) in SMR binary (BESD) format

cage_eqtl_data_hg19.tgz (hg19)

The CAGE eQTL results have finer coverage than the Westra et al. 2013 results with comparable power. Please note that the EGCUT cohort is common to both the Westra et al. 2013 and CAGE data sets. Please see the above link to the CAGE paper that outlines how these eQTL results were generated.

Please see the associated Shiny App for further interactive interrogation of the results generated in the CAGE analysis.

R script and sample file for plot

plot.zip

Update log

1.  24 Aug, 2015: first release.

2.  17 Sept, 2015: updated the format of sparse besd file; added a function to make sparse besd file by extracting information from full dense besd file; added a function to check quickly how many probes are associated with a SNP at p < a threshold(e.g. 5e-8).

3.  12 Oct, 2015: Eigen library and OpenMP were used.

4.   Version 0.6 (10 Nov, 2015): added features of SMR and HEIDI test for the trans regions.

5.   Version 0.619 (4 Aril, 2016): updated sparse besd format; updated features to make sparse verison of BESD; added features to query eQTL summary results; added features to combine BESD files.

6.   Version 0.620 (12 Aril, 2016): added a feature to deal with duplicate IDs.

7.   Version 0.628 (11 May, 2016): added a feature to visualize SMR results.

8.   Version 0.630 (23 May, 2016): updated features to make binary besd file from plain text file(s).

9.   Version 0.631 (23 June, 2016): more options to make BESD files and more memory-efficient when making binary besd files.

10.   Version 0.632 (28 June, 2016): added a feature to make a BESD file from BOLT-LMM output format.

11.   Version 0.64 (8 August, 2016): updated the .esi file format; updated the HEIDI test (a new method that improves the power of the HEIDI test); updated the SMR query output format; improved the analysis to combine multiple BESD files.

12.   Version 0.65 (12 December, 2016): added a flag (--heidi-mtd) for users to choose the original approach or a new approach for HEIDI test.

13.   Version 0.66 (10 January, 2017): updated the function to generate the file for locus plot. The new version is able to read a gene list with/without strand information.

14.   Version 0.67 (22 June, 2017): updated the functions to make BESD file by the following strategy: 1) Z* from N(0, 1) given the p-value. 2) SE* = b / Z* . 3) store b and SE* in BESD. This adjustment guarantees that the re-computed p-value from b and SE being exact the same as the original p-value, useful for data with small sample size.

15.   Version 0.68 (11 August, 2017): updated the SMR and HEIDI tests in the trans regions (the previous version focuses only on the top trans-eQTL locus and the new version will run the tests for all the trans-eQTL loci one at a time).

16.   (12 September, 2017): Luke R. Lloyd-Jones et al. released CAGE eQTL summary statistics for SMR analysis.