snplinkage
Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations
Description
Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.
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CRAN Check Status
Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-macos-arm64 | NOTE |
| r-devel-windows-x86_64 | NOTE |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | NOTE |
| r-release-linux-x86_64 | NOTE |
| r-release-macos-arm64 | NOTE |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | NOTE |
Check details (14 non-OK)
package dependencies
Package required but not available: ‘biomaRt’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
'gtable_ld_associations_combine.Rd' 'gtable_ld_grobs.Rd'
installed package size
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 4.2Mb
installed package size
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 4.2Mb
installed package size
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 4.2Mb
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
*
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
'gtable_ld_associations_combine.Rd' 'gtable_ld_grobs.Rd'
Check History
ERROR 1 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026
package dependencies
Package required but not available: ‘biomaRt’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
'gtable_ld_associations_combine.Rd' 'gtable_ld_grobs.Rd'
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘gtable_ld_associations_combine.Rd’ ‘gtable_ld_grobs.Rd’
DESCRIPTION meta-information
Missing dependency on R >= 4.1.0 because package code uses the pipe
|> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
'gtable_ld_associations_combine.Rd' 'gtable_ld_grobs.Rd'
installed package size
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 4.2Mb
installed package size
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 4.2Mb
installed package size
installed size is 5.6Mb
sub-directories of 1Mb or more:
doc 4.2Mb