Package: IFP 0.2.4

IFP: Identifying Functional Polymorphisms

A suite for identifying causal models using relative concordances and identifying causal polymorphisms in case-control genetic association data, especially with large controls re-sequenced data.

Authors:Park L

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IFP.pdf |IFP.html✨
IFP/json (API)

# Install 'IFP' in R:

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

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

apoe - Genetic data of APOE gene region
apoe7 - Genetic data of APOE gene region
apoeG - Sequencing data of APOE gene region from the 1000 Genomes Project
genoC - Sequencing data of APOE gene region from the 1000 Genomes Project
genoT - Sequencing data of APOE gene region from the 1000 Genomes Project

On CRAN:

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

17 exports 2.57 score 80 dependencies 13 mentions 15 scripts 199 downloads

Last updated 4 years agofrom:9e1e01c849. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 07 2024
R-4.5-win-x86_64	OK	Sep 07 2024
R-4.5-linux-x86_64	OK	Sep 07 2024
R-4.4-win-x86_64	OK	Sep 07 2024
R-4.4-mac-x86_64	OK	Sep 07 2024
R-4.4-mac-aarch64	OK	Sep 07 2024
R-4.3-win-x86_64	OK	Aug 08 2024
R-4.3-mac-x86_64	OK	Aug 08 2024
R-4.3-mac-aarch64	OK	Aug 08 2024

Exports:.lrtB .varEst allele.freq allele.freq.G drgegggne drgegne drgen drgene drggn drgn error.rates geno.freq genotype hap.freq iter.mcmc lrt lrtG

Dependencies:arsenal backports base64enc bslib cachem checkmate cli cluster coda codetools colorspace data.table digest evaluate fansi farver fastmap fontawesome foreign Formula fs ggplot2 glue gridExtra gtable haplo.stats highr Hmisc htmlTable htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling lattice lifecycle magrittr MASS Matrix MatrixModels memoise mgcv mime multcomp munsell mvtnorm nlme nnet pillar pkgconfig polspline quantreg R6 rappdirs RColorBrewer rlang rmarkdown rms rpart rstudioapi sandwich sass scales SparseM stringi stringr survival TH.data tibble tinytex utf8 vctrs viridis viridisLite withr xfun yaml zoo

Citation

Readme and manuals

Help Manual

Help page	Topics
Allele Frequency Computation from Genotype Data	allele.freq
Allele Frequency Computation from the sequencing data with a vcf type of the 1000 Genomes Project	allele.freq.G
Genetic data of APOE gene region	apoe apoe7
Sequencing data of APOE gene region from the 1000 Genomes Project	apoeG genoC genoT
causal models with all possible causal factors: G, GG, GE and E	drgegggne
causal models with three possible causal factors: G, G*E and E	drgegne
causal models with G*E	drgen
causal models with G*E and E	drgene
causal models with G*G	drggn
causal models with G	drgn
Error Rates Estimation for Likelihood Ratio Tests Designed for Identifying Number of Functional Polymorphisms	error.rates
Genotype Frequency Computation from the sequencing data with a vcf type of the 1000 Genomes Project	geno.freq
Conversion to Genotypes from Alleles using the sequencing data with a vcf type of the 1000 Genomes Project	genotype
Estimation of Haplotype Frequencies with Two SNPs	hap.freq
mcmc inference of causal models with all possible causal factors: G, GG, GE and E	iter.mcmc
Likelihood Ratio Tests for Identifying Number of Functional Polymorphisms	lrt
Likelihood Ratio Tests for Identifying Disease Polymorphisms with Same Effects	lrtG

Package: IFP 0.2.4

IFP: Identifying Functional Polymorphisms

Citation

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)