Package: PAST 1.23.0

Thrash Adam

PAST: Pathway Association Study Tool (PAST)

PAST takes GWAS output and assigns SNPs to genes, uses those genes to find pathways associated with the genes, and plots pathways based on significance. Implements methods for reading GWAS input data, finding genes associated with SNPs, calculating enrichment score and significance of pathways, and plotting pathways.

Authors:Thrash Adam [cre, aut], DeOrnellis Mason [aut]

PAST_1.23.0.tar.gz
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PAST.pdf |PAST.html✨
PAST/json (API)
NEWS

# Install 'PAST' in R:

install.packages('PAST', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/igbb/past/issues

On BioConductor:PAST-1.23.0(bioc 3.21)PAST-1.22.0(bioc 3.20)

pathways genesetenrichment

5.70 score 5 stars 7 scripts 162 downloads 2.3k mentions 5 exports 86 dependencies

Last updated 26 days agofrom:926ad93320. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 24 2024
R-4.5-win	WARNING	Nov 24 2024
R-4.5-linux	WARNING	Nov 24 2024
R-4.4-win	WARNING	Nov 24 2024
R-4.4-mac	WARNING	Nov 24 2024
R-4.3-win	WARNING	Nov 24 2024
R-4.3-mac	WARNING	Nov 24 2024

Exports:assign_SNPs_to_genes find_pathway_significance load_GWAS_data load_LD plot_pathways

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bitops cli codetools colorspace cpp11 crayon curl DelayedArray doParallel dplyr fansi farver foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable httr IRanges isoband iterators jsonlite labeling lambda.r lattice lifecycle magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime munsell nlme openssl pillar pkgconfig plyr qvalue R6 RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 vctrs viridisLite withr XML XVector yaml zlibbioc

PAST

Adam Thrash

Rendered frompast.Rmdusingknitr::rmarkdownon Nov 24 2024.

Last update: 2020-03-11
Started: 2019-03-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Assign SNPs in a chunk to genes	assign_chunk
Assign SNPs to genes	assign_SNPs_to_genes
Determine Linkage	determine_linkage
Find Pathway Significance	find_pathway_significance
Find representative SNP for a chunk of SNPs	find_representative_SNP
Find the SNP-gene assignment that represents SNPs assigned to a gene	find_representative_SNP_gene_pairing
Load GWAS data	load_GWAS_data
Load Linkage Disequilibrium	load_LD
Plot Rugplots for Selected Pathways	plot_pathways