Package: snplinkage 1.1.0

snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

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>.

Authors:Thomas Charlon [aut, cre], Karl Forner [aut], Alessandro Di Cara [aut], Jérôme Wojcik [aut]

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snplinkage/json (API)

# Install 'snplinkage' in R:
install.packages('snplinkage', repos = c('https://thomaschln.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://gitlab.com/thomaschln/snplinkage

Datasets:
  • crohn - Crohn's disease data

On CRAN:

30 exports 0.80 score 95 dependencies 13 scripts 875 downloads

Last updated 30 days agofrom:69dee107a5. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 19 2024
R-4.5-winNOTEAug 19 2024
R-4.5-linuxNOTEAug 19 2024
R-4.4-winNOTEAug 19 2024
R-4.4-macNOTEAug 19 2024
R-4.3-winNOTEAug 19 2024
R-4.3-macNOTEAug 19 2024

Exports:%<>%%>%%$%chisq_pvalueschisq_pvalues_gdatadiamond_annotsgdata_add_gene_annotsgdata_add_gene_annots_aim_examplegdata_add_gene_annots_hladr_examplegdata_scans_annotsgdata_snps_annotsget_biomart_metadbggplot_associationsggplot_ldggplot_snp_posgtable_ldgtable_ld_associationsgtable_ld_associations_combinegtable_ld_associations_gdatagtable_ld_gdatagtable_ld_grobsload_gds_as_genotype_dataparallel_applyprint_qc_as_tex_tablesave_hgdp_as_gdsselect_region_idxssnprelate_allele_frequenciessnprelate_ldsnprelate_ld_selectsnprelate_qc

Dependencies:backportsBiobaseBiocGenericsbitbit64blobbootbroomcachemclicliprcodetoolscolorspacecpp11crayondata.tableDBIDNAcopydplyrfansifarverfastmapforcatsforeachformula.toolsgdsfmtgenericsggplot2glmnetgluegtableGWASExactHWGWASToolshavenhmsisobanditeratorsjomolabelinglatticelifecyclelme4lmtestlogistfmagrittrMASSMatrixMatrixModelsmemoisemgcvmiceminqamitmlmunsellnlmenloptrnnetnumDerivoperator.toolsordinalpanpillarpkgconfigplogrprettyunitsprogresspurrrquantregquantsmoothR6RColorBrewerRcppRcppEigenreadrrlangrpartRSQLitesandwichscalesshapeSparseMstringistringrsurvivaltibbletidyrtidyselecttzdbucminfutf8vctrsviridisLitevroomwithrzoo

Other Data Formats And Customizations

Thomas Charlon

Rendered fromcustomize.Rmdusingknitr::rmarkdownon Aug 19 2024.

Last update: 2024-08-19
Started: 2024-08-19

SNP Linkage Disequilibrium Visualizations

Rendered fromsnplinkage.Rnwusingutils::Sweaveon Aug 19 2024.

Last update: 2023-04-30
Started: 2023-04-30

Readme and manuals

Help Manual

Help pageTopics
Assignment pipe%<>%
Pipe%>%
Exposition pipe%$%
Compute Chi-squared p-valueschisq_pvalues
Compute Chi-squared p-values on a Genotype data objectchisq_pvalues_gdata
Crohn's disease datacrohn
Get diamond ggplot layer.diamond_annots
Fetch allele 1 (default object)fetch_allele1.default
Fetch allele 1 (GdsGenotypeReader object)fetch_allele1.GdsGenotypeReader
Fetch allele 1 (GenotypeData object)fetch_allele1.GenotypeData
Fetch allele 1 (GenotypeDataSubset object)fetch_allele1.GenotypeDataSubset
Fetch allele 2 (default object)fetch_allele2.default
Fetch allele 2 (GdsGenotypeReader object)fetch_allele2.GdsGenotypeReader
Fetch allele 2 (GenotypeData object)fetch_allele2.GenotypeData
Fetch allele 1 (GenotypeDataSubset object)fetch_allele2.GenotypeDataSubset
Fetch GDS (default)fetch_gds.default
Fetch GDS (GdsGenotypeReader)fetch_gds.GdsGenotypeReader
Fetch GDS (GenotypeData)fetch_gds.GenotypeData
Fetch GDS (GenotypeDataSubset)fetch_gds.GenotypeDataSubset
gdata_add_gene_annotsgdata_add_gene_annots
gdata_add_gene_annots_aim_examplegdata_add_gene_annots_aim_example
gdata_add_gene_annots_hladr_examplegdata_add_gene_annots_hladr_example
gdata_scan_annotsgdata_scans_annots
gdata_snp_annotsgdata_snps_annots
get_biomart_metadbget_biomart_metadb
Get scans annotations (GenotypeData object)get_scan_annot.GenotypeData
Get scans annotations (GenotypeDataSubset object)get_scan_annot.GenotypeDataSubset
Get SNPs annotations (GenotypeData object)get_snp_annot.GenotypeData
Get SNPs annotations (GenotypeDataSubset object)get_snp_annot.GenotypeDataSubset
Ggplot associationsggplot_associations
Ggplot linkage disequilibriumggplot_ld
Ggplot SNPs positionggplot_snp_pos
Gtable of linkage disequilibrium and chromosomic positionsgtable_ld
Gtable of linkage disequilibrium and associationsgtable_ld_associations
Build gtable by combining ggplotsgtable_ld_associations_combine
Gtable of linkage disequilibrium and associations using a GenotypeData objectgtable_ld_associations_gdata
Gtable of linkage disequilibrium and positions using a GenotypeData objectgtable_ld_gdata
Build gtable by combining ggplotsgtable_ld_grobs
Is SNP first dimension (default)is_snp_first_dim.default
Is SNP first dimension (GDS object)is_snp_first_dim.gds.class
Is SNP first dimension (GdsGenotypeReader object)is_snp_first_dim.GdsGenotypeReader
Is SNP first dimension (GenotypeData object)is_snp_first_dim.GenotypeData
Is SNP first dimension (MatrixGenotypeReader object)is_snp_first_dim.MatrixGenotypeReader
Is SNP first dimension (NcdfGenotypeReader object)is_snp_first_dim.NcdfGenotypeReader
Load GDS as Genotype Dataload_gds_as_genotype_data
Separate a matrix in a list of matrices of length the number of cores and apply a function on the columns in parallelparallel_apply
print_qc_as_tex_tableprint_qc_as_tex_table
save_hgdp_as_gdssave_hgdp_as_gds
select_region_idxsselect_region_idxs
Compute allele frequencie and snp missing ratesnprelate_allele_frequencies
Wrapper for snpgdsLDMat to compute r2snprelate_ld
Wrapper for snpgdsLDpruning to select Tag SNPssnprelate_ld_select
snprelate_qcsnprelate_qc