Hi,
in the function gwasvcf_to_coloc,
the code chunk :
else if (type2 == "cc") {
out2$s <- mean(tab1$NC/tab1$SS, na.rm = TRUE)
}

should be replaced by
if (type2 == "cc") {
out2$s <- mean(tab2$NC/tab2$SS, na.rm = TRUE)
}

#1 the supression of the else statement allow for colocalisation between two case-control traits.
#2 the replacement of tab1 by tab2 allow to get information from the good object.

https://github.com/jrs95/gassocplot

vcfRT <- vcfR::read.vcfR("01_raw_data/confounder/ukb-b-19953.vcf.gz")
Scanning file to determine attributes.
File attributes:
meta lines: 107
header_line: 108
variant count: 9851866
column count: 10
Meta line 107 read in.
All meta lines processed.
gt matrix initialized.
Character matrix gt created.
Character matrix gt rows: 9851866
Character matrix gt cols: 10
skip: 0
nrows: 9851866
row_num: 0
Processed variant: 9851866
All variants processed

data = gwasvcf_to_TwoSampleMR(vcf = vcfRT, type="exposure")
Error in gwasvcf::vcf_to_granges(.) :
Not all inherits(vcf, c("ExpandedVCF", "CollapsedVCF")) are TRUE.

https://github.com/fhormoz/caviar

Since z only have two columns, traits should be a vector of two. So I think there should be a unique function in L70 :

traits <- unique(c(coloclist[["dataset1"]][["id"]], coloclist[["dataset2"]][["id"]]))
names(z) <- traits

Speak to Zoltan about this

https://github.com/gqi/MRMix

https://github.com/rondolab/MR-PRESSO

Dear authors,
I have the following error reporting, are there any hints for this?

# Extract the instruments for HDL cholesterol
gwasvcf::set_bcftools(
  NULL
)
HDL_exp <- gwasvcf::query_gwas(
  "/Users/zhangzhongheng/Documents/2022/GWAS_sepsis/DATA/ieu-b-109.vcf.gz", 
  pval = 5e-10)
HDL_exp <- gwasglue::gwasvcf_to_TwoSampleMR(
  HDL_exp, type="exposure")
#sepsis outcome 
sepsis_out <- gwasvcf::query_gwas(
  "/Users/zhangzhongheng/Documents/2022/GWAS_sepsis/DATA/ieu-b-4982.vcf.gz", 
  rsid = HDL_exp$SNP
    )
'tools_bcftools' option is not set, using native read which may be substantially slower. See 'set_bcftools' for information.
Note, this is much slower than searching by chromosome/position (e.g. see query_chrompos_file)
starting prefilter
prefiltering 12243372 records
Warning: TRE pattern compilation error 'Out of memory'Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'i' in selecting a method for function 'extractROWS': Filter 'fil' failed: invalid regular expression 'rs1191478940|rs1269057460|rs386627425|rs2298214|rs1936360|rs61703480|rs2749141|rs113177974|rs1291065947|rs2144734|rs1457642705|rs664755|rs10737472|rs1558013721|rs2298632|rs649458|rs1198443|rs1212034|rs10753556|rs11340914|rs72654647|rs1370916257|rs147266247|rs961976684|rs60659886|rs1203827760|rs34232231|rs34789477|rs34728853|rs113520491|rs34175245|rs12753981|rs148268445|rs12759594|rs71640337|rs35989952|rs71007882|rs34217609|rs60551503|rs71640338|rs12746810|rs12754468|rs35917448|rs35161452|rs12738345|rs1254174435|rs35738294|rs71636769|rs71636770|rs114165349|rs34585496|rs4579782|rs57217461|rs12743862|rs12744003|rs6666121|rs77408691|rs71514277|rs71007886|rs34423276|rs57532083|rs12737407|rs12737912|rs190077222|rs12729444|rs12726081|rs12730386|rs79568175|rs71581091|rs12726287|rs12756154|rs35407375|rs78533482|rs566260414|rs34517168|rs1369054892|rs800

MRCIEU/gwas2vcf#78

https://github.com/WSpiller/RadialMR

1. Using your vignette, downloading ieu-a-300.vcf.gz ([from (https://gwas.mrcieu.ac.uk/datasets/ieu-a-300/) (also your vignette region, vcffile, bfile and plink-bin)

dat <- gwasvcf_to_finemapr(region = region$region, vcf=vcffile, bfile=bfile, plink_bin=plink_bin)

Extracting data from vcf
Failed to open /Users/dr/Desktop/ieu-a-300.vcf.gz: could not load index
[E::COMPAT_bcf_hdr_read] Input is not detected as bcf or vcf format
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'seqinfo': no 'header' line "#CHROM POS ID..."?

2. Using a vcf file created from gwas txt file

vv %$% create_vcf(chrom=seqnames, pos=start, nea=REF, ea=ALT, snp=ID, ea_af=AF, effect=ES, se=SE, pval=10^-LP, n=SS, name="a")

With same gwasvcf_to_finemapr, following error occurred:

Extracting data from vcf
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'samples': [internal] _hts_rewind() failed

Any help would be appreciated! Thanks

https://github.com/n-mounier/bGWAS

I made 2 vcf files using the gwas2vcf web interface.

When I try and use them with gwasglue, for example:

gtc <- gwasvcf_to_coloc(vcf1, vcf2, chrompos)

I get the error:

Error in unlist_as_integer(x@subscript) : object 'fancy_mseq' not found

This is the same error when I try and do anything with the pkg with these files - do you know what could be causing this?

Thanks!

Trying to do a first-ever install of this package. I'm using R-4.0.0

I did the recommended command: devtools::install_github("mrcieu/gwasglue")
But it failed with:

Error: Failed to install 'gwasglue' from GitHub:
  Failed to install 'gwasvcf' from GitHub:
  HTTP error 404.
  No commit found for the ref master
  
Did you spell the repo owner (`mrcieu`) and repo name (`gwasglue2`) correctly?

I can't help note that final message acts like I type 'gwasglue2' in the command, but I did not include that '2'.

FWIW, I earlier had a "Bad credentials" error, which I got around by creating a GITHUB PAT, so this new error does not seem to be permissions related, as far as I can tell.

Please advise.
Thanks

Installing the package does not work. I have had multiple different issues now:

ERROR: lazy loading failed for package ‘Biostrings’
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Biostrings’
Error: Failed to install 'gwasglue' from GitHub:
  Failed to install 'gwasvcf' from GitHub:
  Failed to install 'Biostrings' from Bioc:
  (converted from warning) installation of package ‘/var/folders/15/564m2q6n7bvdtl7jn8clyxzr0000gn/T//RtmpN2F7eX/file1189c736aeb34/Biostrings_2.56.0.tar.gz’ had non-zero exit status

#10 680.8 ** byte-compile and prepare package for lazy loading
#10 683.5 Error: package or namespace load failed for ‘IRanges’:
#10 683.5  (converted from warning) multiple methods tables found for ‘mstack’
#10 683.5 Error: package ‘IRanges’ could not be loaded
#10 683.5 Execution halted
#10 683.5 ERROR: lazy loading failed for package ‘DelayedArray’
#10 683.5 * removing ‘/usr/local/lib/R/site-library/DelayedArray’
#10 683.9 Error: Failed to install 'gwasglue' from GitHub:
#10 683.9   Failed to install 'gwasvcf' from GitHub:
#10 683.9   Failed to install 'SummarizedExperiment' from Bioc:
#10 683.9   (converted from warning) installation of package ‘DelayedArray’ had non-zero exit status
#10 683.9 Execution halted
#10 ERROR: executor failed running [/bin/sh -c Rscript -e 'devtools::install_github(c("mrcieu/TwoSampleMR", "mrcieu/gwasglue"))']: runc did not terminate sucessfully
```

https://github.com/boxiangliu/locuscomparer

MAF information is missing in several datasets, and colocalisation cannot be performed.
An example:

GWAS <- "ebi-a-GCST005063"
chrpos <- "11:61396322-61796322"
out <- ieugwasr_to_coloc(id1=GWAS, id2=GWAS, chrompos=chrpos)
res <- coloc::coloc.abf(out[[1]], out[[2]])
Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) :
0 (non-NA) cases
Inoltre: Warning message:
In sdY.est(d$varbeta, d$MAF, d$N) :
estimating sdY from maf and varbeta, please directly supply sdY if known

Coloc recommends to only run tests on loci with 50 SNPs or more so I included a filter.

w1<-which(out[[1]]$varbeta==Inf|out[[2]]$varbeta=="Inf")
length(out[[1]]$snp)

for (k in 1:length(n)){
out[[1]][[k]]<-out[[1]][[k]][-w1]
out[[2]][[k]]<-out[[2]][[k]][-w1]
}

out <- gwasvcf_to_coloc(vcf1=paste0(path2,eqtl.traits[tr],"/",eqtl.traits[tr],".vcf.gz"),vcf2=paste0(path,trait[i],".harmonized.vcf.gz"),chrompos=chrpos)

w1<-which(out[[1]]$varbeta==Inf|out[[2]]$varbeta=="Inf")
length(out[[1]]$snp)

for (k in 1:length(n)){
out[[1]][[k]]<-out[[1]][[k]][-w1]
out[[2]][[k]]<-out[[2]][[k]][-w1]
}

length(out[[1]]$snp)

if(length(out[[1]]$snp)>50& length(out[[2]]$snp)>50) {
res <- coloc::coloc.abf(out[[1]], out[[2]])

https://cran.r-project.org/web/packages/MendelianRandomization/index.html

top <- ieugwasr::tophits('ieu-a-300',p=5e-8) %>% arrange(p)
chrpos <- paste0(top$chr[1], ":", top$position[1] - 90000, "-", top$position[1] + 90000)
out <- ieugwasr_to_coloc(id1='ieu-a-300', id2='eqtl-a-ENSG00000270172', chrompos=chrpos)
Error in if (type1 == "cc") { : missing value where TRUE/FALSE needed

http://cnsgenomics.com/software/gsmr/

Hi, there:

I am very glad to see that you guys are building an ecosystem for VCF formatted GWAS files.

There are 4 new tools, all published this year. I tested and found them very easy to implement and quite important for functional analyses. It would be great if you guys could consider adding them.

1. For genetic architecture, iCPAGdb, published at Genome Medicine: "An atlas connecting shared genetic architecture of human diseases and molecular phenotypes provides insight into COVID-19 susceptibility".

2. For colocalization, hyprcoloc, published at Nature Communications: "A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits".

3. For drug target analysis (maybe add as a new category), Trans-Phar, published at Human Molecular Biology: “Integration of genetically regulated gene expression and pharmacological library provides therapeutic drug candidates".

4. For enrichment analysis (maybe add as a new category "enrichment"), clusterProfiler, published at The Innovation: "clusterProfiler 4.0: A universal enrichment tool for interpreting omics data".

Finally, I feel it is very important to add a new category for (cross-traits) meta-analysis. A lot of reserachers would want to do this when a lot of GWAS are available. This includes the traditional MTAG software, a new PLEIO software published this year at AJHG: "a method to map and interpret pleiotropic loci with GWAS summary statistics"

Best regards,
Jie

In eQTL Gen some of the zscores/varbeta in the out list were NA. For example, eqtl-a-ENSG00000002834. This resulted in NA in the coloc test. This happens quite a lot. Not sure why.

https://github.com/hakyimlab/MetaXcan

Is it possible to add GTEX eQTL to MRBase?

Dear Gib,

is there a way to install the gwasglue package without the finemapr package? I have issues installing the finemapr one:

Error: Failed to install 'gwasglue' from GitHub:
Failed to install 'finemapr' from GitHub:
(converted from warning) installation of package ‘/var/folders/4l/wx5nz34j4k5064xcw4wf0vk80000gp/T//RtmpdUQ8Po/file54b310ffff77/finemapr_0.1.0.tar.gz’ had non-zero exit status

Many thanks,
Verena

Dear Team,

I am wondering how challenging it will be if I replace all the hg19 data/reference/annotation to hg38 for gwasglue workflow?

Thanks

Shicheng

Hey,

I'm interested in using GWASVCF files to run LDSC. Seems like the best way to do it would be to create a gwasvcf_to_ldsc function here, right?

Wondering if you've had a go at doing this yet? Got any tips on setting it up? LDSC will expect the gwasvcf to be converted to a standard sumstats format (SNP CHR BP A1 A2 P Z): have you got any example code for doing this?

Thanks

Tagging in: @Al-Murphy @roxyisat-rex

https://github.com/pjnewcombe/R2BGLiMS

Dear Team,

I am wondering whether coloc version 5 has been implemented into the workflow? or coloc version 4 is applied.

Thanks.

Shicheng