Package: fcfdr 1.0.0

fcfdr: Flexible cFDR

Provides functions to implement the Flexible cFDR (Hutchinson et al. (2021) <doi:10.1371/journal.pgen.1009853>) and Binary cFDR (Hutchinson et al. (2021) <doi:10.1101/2021.10.21.465274>) methodologies to leverage auxiliary data from arbitrary distributions, for example functional genomic data, with GWAS p-values to generate re-weighted p-values.

Authors:Anna Hutchinson [aut, cre], Chris Wallace [aut], Thomas Willis [ctb, aut], James Liley [ctb]

fcfdr_1.0.0.tar.gz
fcfdr_1.0.0.zip(r-4.7)fcfdr_1.0.0.zip(r-4.6)fcfdr_1.0.0.zip(r-4.5)
fcfdr_1.0.0.tgz(r-4.6-any)fcfdr_1.0.0.tgz(r-4.5-any)
fcfdr_1.0.0.tar.gz(r-4.7-any)fcfdr_1.0.0.tar.gz(r-4.6-any)
fcfdr_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fcfdr/json (API)

# Install 'fcfdr' in R:

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

Bug tracker:https://github.com/annahutch/fcfdr/issues

Datasets:

T1D_application_data - Data for T1D application

On CRAN:

5.42 score 6 stars 11 scripts 233 downloads 7 exports 83 dependencies

Last updated from:c2e73698a1. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	198
source / vignettes	OK	1044
linux-release-x86_64	OK	188
macos-release-arm64	OK	243
macos-oldrel-arm64	OK	181
windows-devel	OK	156
windows-release	OK	174
windows-oldrel	OK	192
wasm-release	OK	132

Exports:binary_cfdr corr_plot flexible_cfdr log10pv_plot parameters_in_locfdr pv_plot stratified_qqplot

Dependencies:backports base64enc bigsplines bslib cachem checkmate cli cluster colorspace cowplot cpp11 data.table deldir digest dotCall64 dplyr evaluate farver fastmap fields fontawesome foreign Formula fs generics ggplot2 glue gridExtra gtable hexbin highr Hmisc htmlTable htmltools htmlwidgets isoband jquerylib jsonlite knitr labeling lattice lifecycle locfdr magrittr maps MASS Matrix memoise mime nnet pillar pkgconfig polyclip polyCub quadprog R6 rappdirs RColorBrewer Rcpp rlang rmarkdown rpart rstudioapi S7 sass scales sp spam spatstat.data spatstat.geom spatstat.univar spatstat.utils stringi stringr tibble tidyselect tinytex utf8 vctrs viridisLite withr xfun yaml

Introductory vignette

Simple walk-through example

Rendered fromfcfdr-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-02-08
Started: 2020-09-21

T1D Application

Rendered fromt1d_app.Rmdusingknitr::rmarkdown

Last update: 2022-02-08
Started: 2020-10-19

Extra Information

Contents | Genomic control | Auxiliary data | Finding independent subsets of SNPs | Applying cFDR iteratively

Rendered fromextra-information.Rmdusingknitr::rmarkdown

Last update: 2022-02-07
Started: 2020-11-16

LDAK vignette

Optional: Obtaining and processing the 1000G data | Joining the 1000G and GWAS SNPs | Running the LDAK weighting calculation procedure | Using the LDAK weightings in flexible_fcfdr

Rendered fromldak-vignette.Rmdusingknitr::rmarkdown

Last update: 2022-02-07
Started: 2021-04-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Perform cFDR leveraging binary auxiliary covariates	binary_cfdr
Violin plot of p-values for quantiles of q	corr_plot
Perform Flexible cFDR	flexible_cfdr
Plot -log10(p) against -log10(v) and colour by q	log10pv_plot
Function to downsample independent SNPs to match MAF distribution of whole set.	match_ind_maf
parameters_in_locfdr	parameters_in_locfdr
Plot p against v and colour by q	pv_plot
Stratified Q-Q plot.	stratified_qqplot
Data for T1D application	T1D_application_data