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CASMAP (version 0.6.1)

Detection of Statistically Significant Combinations of SNPs in Association Mapping

Description

A significant pattern mining-based toolbox for region-based genome-wide association studies and higher-order epistasis analyses, implementing the methods described in Llinares-Lpez et al. (2017) .

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Version

Install

install.packages('CASMAP')

Monthly Downloads

67

Version

0.6.1

License

GPL (>= 2)

Maintainer

Dean Bodenham

Last Published

May 5th, 2020

Functions in CASMAP (0.6.1)

getExampleDataFilename

Get the path to the example data file for regionGWAS mode

getExampleLabelsFilename

Get the path to the example labels file for regionGWAS mode

lib_delete_search_chi

Internal function

SignificantIntervalSearchFastCmh-class

Fast significant interval search with categorical covariates

lib_delete_search_e

Internal function

isInOpenInterval

A method to check value is numeric and in open interval

isRegionGWASString

Checks if substring is part of regionGWAS

lib_new_search_chi

Internal function

lib_get_result_facs

Internal function

SignificantIntervalSearchExact-class

Internal class for search for significant regions

SignificantItemsetSearchFacs-class

Significant itemsets search with categorical covariates

SignificantIntervalSearchChi-class

Approximate fast significant interval search

lib_delete_search_fastcmh

Internal function

lib_delete_search_facs

Internal function

lib_filter_intervals_write_to_file

Internal function

lib_new_search_e

Internal function

getExampleSignificantRegionsFilename

Get the path to the example significant intervals file

lib_get_result_fais

Internal function

Constructor for CASMAP class object.

lib_pvals_significant_ints_write_to_file

Internal function

getHigherOrderEpistasisString

Gets the higherOrderEpistasis string

Global variables environment

lib_pvals_significant_isets_write_to_file

Internal function

lib_read_plink_files

Internal function

getParentFunctionName

Get the function name

lib_get_result_iset

Internal function

getMinModeLength

Gets the minModeLength

lib_profiler_write_to_file

Internal function

isHigherOrderEpistasisString

Checks if substring is part of higherOrderEpistasis

lib_execute_int

Internal function

lib_get_significant_itemsets

Internal function

lib_read_plink_files_with_cov_facs

Internal function

lib_get_result_int

Internal function

lib_get_filtered_intervals

Internal function

lib_execute_iset

Internal function

lib_get_significant_intervals

Internal function

lib_write_eth_files_with_cov_facs

Internal function

getRegionGWASString

Gets the regionGWAS string

lib_pvals_testable_ints_write_to_file

Internal function

lib_read_eth_files_with_cov_fastcmh

Internal function

lib_read_plink_files_with_cov_fastcmh

Internal function

lib_new_search_facs

Internal function

lib_read_eth_files_with_cov_facs

Internal function

lib_summary_write_to_file_fais

Internal function

lib_summary_write_to_file_facs

Internal function

lib_new_search_fastcmh

Internal function

m_SignificantIntervalSearchFais-class

lib_summary_write_to_file_fastcmh

Internal function

m_SignificantIntervalSearch-class

modeLengthErrorMessage

Error message for mode, if too short

modeNeedsMoreChars

Checks mode string is long enough

lib_write_eth_files_with_cov_fastcmh

Internal function

lib_read_covariates_file_fastcmh

Internal function

lib_write_eth_files_int

Internal function

lib_write_eth_files_iset

Internal function

lib_read_eth_files

Internal function

lib_pvals_testable_isets_write_to_file

Internal function

lib_read_covariates_file_facs

Internal function

m_SignificantFeaturesSearch-class

m_SignificantItemsetSearch-class

m_SignificantFeaturesSearchWithCovariates-class

modeErrorMessage

Error message for mode

getExampleCovariatesFilename

Get the path to the example covariates file for regionGWAS mode

Check if a variable is boolean or not