Package: CASMAP 0.6.1

Dean Bodenham

CASMAP: Detection of Statistically Significant Combinations of SNPs in Association Mapping

A significant pattern mining-based toolbox for region-based genome-wide association studies and higher-order epistasis analyses, implementing the methods described in Llinares-López et al. (2017) <doi:10.1093/bioinformatics/btx071>.

Authors:Felipe Llinares-López [aut, cph], Laetitia Papaxanthos [aut, cph], Damian Roqueiro [aut, cph], Matthew Baker [ctr], Mikołaj Rybiński [ctr], Uwe Schmitt [ctr], Dean Bodenham [aut, cre, cph], Karsten Borgwardt [aut, fnd, cph]

CASMAP_0.6.1.tar.gz
CASMAP_0.6.1.tar.gz(r-4.5-noble)CASMAP_0.6.1.tar.gz(r-4.4-noble)
CASMAP_0.6.1.tgz(r-4.4-emscripten)CASMAP_0.6.1.tgz(r-4.3-emscripten)
CASMAP.pdf |CASMAP.html✨
CASMAP/json (API)

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 9 scripts 165 downloads 64 exports 1 dependencies

Last updated 5 years agofrom:9541eb5644. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-linux-x86_64NOTEOct 28 2024

Exports:CASMAPCASMAPenvcheckIsBooleangetExampleCovariatesFilenamegetExampleDataFilenamegetExampleLabelsFilenamegetExampleSignificantRegionsFilenamegetHigherOrderEpistasisStringgetMinModeLengthgetParentFunctionNamegetRegionGWASStringisHigherOrderEpistasisStringisInOpenIntervalisRegionGWASStringlib_delete_search_chilib_delete_search_elib_delete_search_facslib_delete_search_fastcmhlib_execute_intlib_execute_isetlib_filter_intervals_write_to_filelib_get_filtered_intervalslib_get_result_facslib_get_result_faislib_get_result_intlib_get_result_isetlib_get_significant_intervalslib_get_significant_itemsetslib_new_search_chilib_new_search_elib_new_search_facslib_new_search_fastcmhlib_profiler_write_to_filelib_pvals_significant_ints_write_to_filelib_pvals_significant_isets_write_to_filelib_pvals_testable_ints_write_to_filelib_pvals_testable_isets_write_to_filelib_read_covariates_file_facslib_read_covariates_file_fastcmhlib_read_eth_fileslib_read_eth_files_with_cov_facslib_read_eth_files_with_cov_fastcmhlib_read_plink_fileslib_read_plink_files_with_cov_facslib_read_plink_files_with_cov_fastcmhlib_summary_write_to_file_facslib_summary_write_to_file_faislib_summary_write_to_file_fastcmhlib_write_eth_files_intlib_write_eth_files_isetlib_write_eth_files_with_cov_facslib_write_eth_files_with_cov_fastcmhm_SignificantFeaturesSearchm_SignificantFeaturesSearchWithCovariatesm_SignificantIntervalSearchm_SignificantIntervalSearchFaism_SignificantItemsetSearchmodeErrorMessagemodeLengthErrorMessagemodeNeedsMoreCharsSignificantIntervalSearchChiSignificantIntervalSearchExactSignificantIntervalSearchFastCmhSignificantItemsetSearchFacs

Dependencies:Rcpp

Introduction to CASMAP

Dean Bodenham

Rendered fromintro.Rmdusingknitr::rmarkdownon Oct 28 2024.

Last update: 2018-07-05
Started: 2018-07-05