| Type: | Package |
| Title: | Functional Genomics Repository for POST-GWAS Analysis |
| Version: | 1.3.2.0 |
| Date: | 2024-11-07 |
| Author: | Alireza Ani [aut, cre], Ahmad Vaez [aut] |
| Maintainer: | Alireza Ani <a.ani@umcg.nl> |
| Depends: | R (≥ 3.5) |
| Description: | A collection of datasets essential for functional genomic analysis. Gene names, gene positions, cytoband information, sourced from Ensembl and phenotypes association graph prepared from GWAScatalog are included. Data is available in both GRCh37 and 38 builds. These datasets facilitate a wide range of genomic studies, including the identification of genetic variants, exploration of genomic features, and post-GWAS functional analysis. |
| License: | GPL-3 |
| Encoding: | UTF-8 |
| LazyData: | true |
| LazyDataCompression: | xz |
| RoxygenNote: | 7.3.2 |
| NeedsCompilation: | no |
| Packaged: | 2024-11-07 06:27:56 UTC; Alireza |
| Repository: | CRAN |
| Date/Publication: | 2024-11-08 15:10:12 UTC |
GWAScatalog graph
Description
A graph object of GWAScatalog data. The association between variants and phenotypes are indicated.
Usage
GWASCat_graph
Format
An object of igraph class.
Source
GWAS Catalog, https://www.ebi.ac.uk/gwas
References
Sollis, E, et al. (2022). The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Research, 51, Pages D977–D985. doi:10.1093/nar/gkac1010
Examples
data(GWASCat_graph)
Cytoband information (GRCh37)
Description
A dataset containing cytoband information based on GRCh37.
Usage
cytoband_grch37
Format
A data frame with 4 columns:
- chr
chromosome
- start
start position
- end
end position
- band
band name
Source
Ensembl, https://www.ensembl.org
References
Harrison, PW, et al. (2024). Ensembl 2024. Nucleic Acids Research, 52, Pages D891–D899. doi:10.1093/nar/gkad1049
Examples
data(cytoband_grch37)
Cytoband information (GRCh38)
Description
A dataset containing cytoband information based on GRCh38.
Usage
cytoband_grch38
Format
A data frame with 4 columns:
- chr
chromosome
- start
start position
- end
end position
- band
band name
Source
Ensembl, https://www.ensembl.org
References
Harrison, PW, et al. (2024). Ensembl 2024. Nucleic Acids Research, 52, Pages D891–D899. doi:10.1093/nar/gkad1049
Examples
data(cytoband_grch38)
Gene Names (GRCh37)
Description
A dataset containing gene names based on GRCh37.
Usage
gene_names_grch37
Format
A data frame with 6 columns:
- id
Gene identifier
- name
Gene name
- chr
Chromosome
- start
Start position
- end
End position
- type
Gene type
Source
Ensembl, https://www.ensembl.org
References
Harrison, PW, et al. (2024). Ensembl 2024. Nucleic Acids Research, 52, Pages D891–D899. doi:10.1093/nar/gkad1049
Examples
data(gene_names_grch37)
Gene Names (GRCh38)
Description
A dataset containing gene names based on GRCh38.
Usage
gene_names_grch38
Format
A data frame with 6 columns:
- id
Gene identifier
- name
Gene name
- chr
Gene name
- start
Gene name
- end
Gene name
- type
Gene name
Source
Ensembl, https://www.ensembl.org
References
Harrison, PW, et al. (2024). Ensembl 2024. Nucleic Acids Research, 52, Pages D891–D899. doi:10.1093/nar/gkad1049
Examples
data(gene_names_grch38)