The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.

CoPheScan: Input data

Ichcha Manipur

2024-03-11

The input dataset for a trait (querytrait) should contain the summary data for SNPs in a genomic region around the query variant (querysnpid) and should have the following fields:

For a Case-control dataset

beta: \(\beta\) or effect size

varbeta: variance of \(\beta\) or square of the standard error of \(\beta\)

snp: SNP identifier which maybe rsid or CHR_BP_REF_ALT or CHR_BP

type:‘cc’

N: sample size

For a Quantitave dataset

When, beta and varbeta are not available the following

beta: \(\beta\) or effect size

varbeta: variance of \(\beta\) or square of the standard error of \(\beta\)

snp: SNP identifier which maybe rsid or CHR_BP_REF_ALT or CHR_BP

type:‘quant’

N: sample size

sdY: for a quantitative trait, the population standard deviation of the trait.

Additional fields in case of missing beta/varbeta or sdY

MAF: Minor allele frequency (only required when either beta/varbeta or sdY are unavailable)

pvalues: only required when beta/varbeta are unavailable

s: fraction of samples that are cases (only for a case-control trait when beta/varbeta are unavailable)

library(cophescan)

Explore the data structure of the example dataset available in the cophescan package

data("cophe_multi_trait_data")
trait_dat = cophe_multi_trait_data$summ_stat$Trait_1
str(trait_dat)
#> List of 8
#>  $ beta   : Named num [1:1000] -0.01369 0.01666 0.09057 -0.00571 -0.05606 ...
#>   ..- attr(*, "names")= chr [1:1000] "chr19-11173352" "chr19-11173626" "chr19-11173716" "chr19-11173807" ...
#>  $ varbeta: Named num [1:1000] 0.000516 0.000399 0.003124 0.000419 0.000473 ...
#>   ..- attr(*, "names")= chr [1:1000] "chr19-11173352" "chr19-11173626" "chr19-11173716" "chr19-11173807" ...
#>  $ z      : Named num [1:1000] -0.603 0.834 1.62 -0.279 -2.578 ...
#>   ..- attr(*, "names")= chr [1:1000] "chr19-11173352" "chr19-11173626" "chr19-11173716" "chr19-11173807" ...
#>  $ snp    : chr [1:1000] "chr19-11173352" "chr19-11173626" "chr19-11173716" "chr19-11173807" ...
#>  $ MAF    : Named num [1:1000] 0.2614 0.4871 0.0318 0.4046 0.3042 ...
#>   ..- attr(*, "names")= chr [1:1000] "chr19-11173352" "chr19-11173626" "chr19-11173716" "chr19-11173807" ...
#>  $ type   : chr "cc"
#>  $ N      : num 20000
#>  $ s      : num 0.5

Additional field for cophe.susie

LD: Linkage Disequilibrium matrix with row and column names being the same as the snp field.

trait_dat$LD = cophe_multi_trait_data$LD
str(trait_dat$LD[1:10, 1:10])
#>  num [1:10, 1:10] 1 0.0267 -0.1078 -0.0627 0.1033 ...
#>  - attr(*, "dimnames")=List of 2
#>   ..$ : chr [1:10] "chr19-11173352" "chr19-11173626" "chr19-11173716" "chr19-11173807" ...
#>   ..$ : chr [1:10] "chr19-11173352" "chr19-11173626" "chr19-11173716" "chr19-11173807" ...

It is important to check that there is alignment of alleles for which the beta is reported and those in the LD matrix. This can be verified either using coloc::check_alignment or performing a diagnostic check using the susie package https://stephenslab.github.io/susieR/articles/susierss_diagnostic.html.

Note

The input summary data structure for a trait is the same format as required by coloc. To gain a detailed understanding of the input please see the coloc vignette https://chr1swallace.github.io/coloc/articles/a02_data.html and the test datasets provided with the coloc package.
More information on the input can be obtained from the coloc documentation : ?coloc::check_dataset

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.