From 585448d9ceecaab016801851439122ac6b0d7d55 Mon Sep 17 00:00:00 2001
From: William Ryan <billyryan543@gmail.com>
Date: Tue, 14 May 2024 11:56:58 -0400
Subject: [PATCH] Add KEGG example data

Update readme with links.
---
 R/data.R              |  14 ++++++++++++++
 README.Rmd            |   2 +-
 data/kegg_example.rda | Bin 0 -> 1856 bytes
 man/kegg_example.Rd   |  24 ++++++++++++++++++++++++
 4 files changed, 39 insertions(+), 1 deletion(-)
 create mode 100644 data/kegg_example.rda
 create mode 100644 man/kegg_example.Rd

diff --git a/R/data.R b/R/data.R
index fbdca1f..5a3325e 100644
--- a/R/data.R
+++ b/R/data.R
@@ -13,3 +13,17 @@
 #'
 #' @source <https://doi.org/10.1038/s41380-021-01205-y>
 "gsea_example"
+
+#' An example of KEGG results
+#'
+#' A wide data frame with enrichment scores (log10 FDR) from
+#' MetaboAnalyst of one comparison.
+#'
+#' @format A data frame with 183 rows and 2 columns:
+#' \describe{
+#' \item{MAP}{KEGG Pathway IDS}
+#' \item{MA}{Enrichment Scores of KEGG pathways}
+#' }
+#'
+#' @source <https://doi.org/10.1101/2023.10.13.562226>
+"kegg_example"
diff --git a/README.Rmd b/README.Rmd
index 2528376..4d18a37 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -32,7 +32,7 @@ remotes::install_github("willgryan/PAVER")
 
 ## Usage
 
-PAVER is designed to work with the output of pathway analysis tools. The package includes a vignette with an example dataset that explains it's functionality.
+PAVER is designed to work with the output of pathway analysis tools. The package includes a vignette with an example dataset that explains it's functionality. The R Shiny application for the PAVER R package is hosted at [https://cdrl.shinyapps.io/PAVER/](https://cdrl.shinyapps.io/PAVER/). For more detailed information on PAVER and its functionalities, please refer to the article on the Cognitive Disorders Research Laboratory (CDRL) website [here](https://cdrl-ut.org/project/projects_and_posters/paver/).
 
 ## Contributing
 
diff --git a/data/kegg_example.rda b/data/kegg_example.rda
new file mode 100644
index 0000000000000000000000000000000000000000..0863f1356f4238db78963e3454ecc6a3d4d303a8
GIT binary patch
literal 1856
zcmV-G2fz6JH+ooF0004LBHlIv03iV!0000G&sfah5*Y^qT>vQ&2UJ%g<Ze>RpOV=m
zY?7$Lk2$RQ4ScfyUE#9Vj26AeT)?W^gyiBtgY{~`T)I_b7fFk@`Z1YrDYkz4lsG&i
zf}~6jdCjp|1y*;+VK;ws+>jzuqg=UJo!@!vQn)4T0;484RW>P7Q<8@Sw@18LG@tro
zUM{09hUsmF%~xM=GM3UP;(%g(RUC5_`{t6AtWb<2edBpLO6YEnia-X~+%|rkS8|mV
zp;<%>Vpl~+VY6=5`ALeKWRNX;J$;w<ZJt=v{g{HR^CT&9i>!nd+&P>3d^tA=ot8p%
zV<9#?q6{&XFk|tc!TZ&vF5cYWXi71o5WlA33wQhL`?=*_(Foab97_VLs*CFJCcF|y
zU|^uD42XZPk)R)JkY}N(X$Z(l0`%tY#H}d?-VeNoeJq+Qif9bI;?v5_N5&a`EktvR
z|AfxbVo`{u?|dT<A4*f2#zZvy7o4TAW84rkFpf05TvQp^;0!^63s3}!93gNl#yB-A
z#`sJ)&wRvuX6~vDiN12as0?;b*p`z%EZrL#)I(l)R74_C_RmBxH_DLh+yq@=IW=&9
znlQ|3FD(4}l9nI49P@R1FhO!CuTNUnZyi833J%9CS6~jTw_x!w!02J(=Cs74r0txB
zp9sUZ>%9!iBzjY37Mi3IQGg5fIZ7>>F;;)LrnDQR3f+s7tXyhbN2Q&kO+(0mbvCW(
zoJppIODOnFJxck<_+e|auhU2^DW$+N`~jq>&@#-wT*j0`AwZH?4MpyhCz-lSxvaYN
z_SMy8NR}0dA{)U=B5vIs!`E|p#Z}jvneKOEzVGL;OAE50foV^I7*?L&*f>+?FcZ!x
zG!v|1&>WeI>t`kjE}2F~&MJGDJB9*#EuHW*OBC7hkWCYrVT#ELF`>o!9vqqb98jGz
z?Bj;yB+@4vBDcd50elj<o16rY2<Yw;3xTTs_?M^6kva~%iDF)f6)<WJa9|2iYq5TW
zt2b+A=^*1KTWZ<r-`C`}t&l<Baj0~*3bo!B={OH(MpX7BTneS~#e;*+GqVgQ5aHw_
z21K0B6@}5pe1A1FkPGb#U;9=KM}N{t6o{iU;gaoF93*LflHO$tH;?@ieo><!r4EIN
zN-ci&6R-~rsJ{pJYAQL&<NG*A=)5wBkY%`7dhhwE#+q!m#POhY`o_?*<sPX@zGeh&
za(@lq7Hs-rA*A$bH?42`(9G%*);E5DB7FVCvb_cLkQvAee-O<OZ3V*HA^jBfKc~^?
z>fqVuneX^vbt|2T{bq!v_rtjF;^&W(td?IS1qh)2Vt&>=3FW*Sc`XxG0iid6FT<#S
zVI<tIsfDX%?a?<7=NI6CfTH~I2)Z6r=5}Ghd&<f$elLef^eXa%#4MA~K5H%->mp`0
zen7WPVrEu1T$!jYOKK>0f}k+Mu#H55Aqzd8ovjcZaX=iDFq`3=43lNR6B=<AK#J#w
zBSMZi#I`l*&#>t*a<o6q{Vu0$i#Y%W3_D!b@DTUOAmdmhtn-8W$iHj}jZs$U>3&_d
zdz;8s$-<V<Y!k=Ptd^C;JHIrXOYw~f)FO5PDG#Z?vB>My6qnwd&sIrmBy+8KUFIP4
z<%utSTRokG?N%567A#=azR(PzCrz_ZaeWB5X6l3}gzXW(aYk4wBbhI?E5(0iKvU4r
zo`}!xjP)D*!InIAsrAW5ca<?zbO+ts^e#d7nr!Il@#4NLSW9CV-v6O|N?G87cXudh
z`w{J_FEf9gF;ow6B4<pI(S!DYW#p~CPmq_?C2NkL^$H$zYI%A)dyU!xWALSCidFRw
znuHjjT&?CerUHLDQt_A6<L6eCaf}KiK+{}Csh>lmK}hlT5=1Xk@dc5mE<vE;F&l%I
zvD{M@<B(#`fL8bnmQ@oVr-xSK^cXI;hkjr3%=cZe`4hdppy-a-^(gM6>wrzV3`lqq
zLdDb^IX|$~#rq#nfN*WpSmYrgJemw!j|nVcK8R7__j6#Yh2RJoU^`){T@B_5IzCd3
z!U5JeE~S{v(dceL9@WgaYISv!S4e$yS&c?`#{jRViFrPOntz{Pp-30r*1G${!p(}J
zT;!E!eUG0J@G-8WSZ#195OA8=0=eX}Btz4WBl|Vd(pk)Zlr~HEB(?x!a&9Y2<*NU=
zgv;j5MHnXIjD)lbnD>PRmXk_ad+cZx&2<5<{X)b=<iSSZ$9+eq&ZO#}gtpOiq1{NY
z|NUiz&GdEt3_aRcVx1RVQ@_fix&y_2gz8(jq1UR{4^L_^dZcXR9+FFfMM3&!`PJYe
zlfqz8`^!#Q!aJ)dQz>LTm2a?(g3|fh^-Fp!mo38d2hHuBI{aId%k_1zL1_r@O^&R9
uMasJ_#}HJFqNcC_0002mfkadQ0h$h)Bme+qupuozFb#_W000000a;qzzm5$6

literal 0
HcmV?d00001

diff --git a/man/kegg_example.Rd b/man/kegg_example.Rd
new file mode 100644
index 0000000..e6a3f2e
--- /dev/null
+++ b/man/kegg_example.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data.R
+\docType{data}
+\name{kegg_example}
+\alias{kegg_example}
+\title{An example of KEGG results}
+\format{
+A data frame with 183 rows and 2 columns:
+\describe{
+\item{MAP}{KEGG Pathway IDS}
+\item{MA}{Enrichment Scores of KEGG pathways}
+}
+}
+\source{
+\url{https://doi.org/10.1101/2023.10.13.562226}
+}
+\usage{
+kegg_example
+}
+\description{
+A wide data frame with enrichment scores (log10 FDR) from
+MetaboAnalyst of one comparison.
+}
+\keyword{datasets}