hscovar
Calculation of Covariance Between Markers for Half-Sib Families
Description
The theoretical covariance between pairs of markers is calculated from either paternal haplotypes and maternal linkage disequilibrium (LD) or vise versa. A genetic map is required. Grouping of markers is based on the correlation matrix and a representative marker is suggested for each group. Employing the correlation matrix, optimal sample size can be derived for association studies based on a SNP-BLUP approach. The implementation relies on paternal half-sib families and biallelic markers. If maternal half-sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. Wittenburg, Bonk, Doschoris, Reyer (2020) "Design of Experiments for Fine-Mapping Quantitative Trait Loci in Livestock Populations" <doi:10.1186/s12863-020-00871-1>. Carlson, Eberle, Rieder, Yi, Kruglyak, Nickerson (2004) "Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium" <doi:10.1086/381000>.
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Check details (14 non-OK)
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examples
Running examples in ‘hscovar-Ex.R’ failed
The error most likely occurred in:
> ### Name: tagSNP
> ### Title: tagSNP
> ### Aliases: tagSNP
>
> ### ** Examples
>
> ### 1: INPUT DATA
> data(testdata)
> ### 2: COVARIANCE/CORRELATION MATRIX
> corrmat <- CovMat(matLD, H.sire, 100, pos.chr, corr = TRUE)
*** caught segfault ***
address 0x110, cause 'invalid permissions'
Traceback:
1: lapply(X = S, FUN = FUN, ...)
2: doTryCatch(return(expr), name, parentenv, handler)
3: tryCatchOne(expr, names, parentenv, handlers[[1L]])
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call, nlines = 1L) prefix <- paste("Error in", dcall, ": ") LONG <- 75L sm <- strsplit(conditionMessage(e), "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && isTRUE(getOption("show.error.messages"))) { cat(msg, file = outFile) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
6: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
7: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
8: FUN(X[[i]], ...)
9: lapply(seq_len(cores), inner.do)
10: mclapply(e1, tcrossprod)
11: CovarMatrix(expectationMat, linkMat, linkSire, Ns)
12: CovMat(matLD, H.sire, 100, pos.chr, corr = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Warning in mclapply(e1, tcrossprod) :
scheduled core 1 did not deliver a result, all values of the job will be affected
0 SNPs have non-zero variance -> output matrix has reduced dimensions.
Error in `rownames<-`(`*tmp*`, value = 1:p) :
attempt to set 'rownames' on an object with no dimensions
Calls: CovMat -> rownames<-
Execution halted
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Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026
examples
Running examples in ‘hscovar-Ex.R’ failed The error most likely occurred in: > ### Name: tagSNP > ### Title: tagSNP > ### Aliases: tagSNP > > ### ** Examples > > ### 1: INPUT DATA > data(testdata) > ### 2: COVARIANCE/CORRELATION MATRIX > corrmat <- CovMat(matLD, H.sire, 100, pos.chr, corr = TRUE) *** caught segfault *** address 0x110, cause 'invalid permissions' Traceback: 1: lapply(X = S, FUN = FUN, ...) 2: doTryCatch(return(expr), name, parentenv, handler) 3: tryCatchOne(expr,