version 1.3

DESCRIPTION

@@ -1,21 +1,21 @@
 Package: POINT
 Type: Package
 Title: Protein Structure Guided Local Test
-Version: 1.2
-Date: 2022-06-05
+Version: 1.3
+Date: 2023-10-01
 Author: Rachel Marceau West, Shannon T. Holloway
 Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
 Description: Provides an implementation of a rare variant association test that utilizes protein tertiary structure to increase signal and to identify likely causal variants. Performs structure-guided collapsing, which leads to local tests that borrow information from neighboring variants on a protein and that provide association information on a variant-specific level. For details of the implemented method see West, R. M.,  Lu, W., Rotroff, D. M., Kuenemann, M., Chang, S-M., Wagner M. J., Buse, J. B., Motsinger-Reif, A., Fourches, D., and Tzeng, J-Y. (2019) <doi:10.1371/journal.pcbi.1006722>.
 License: GPL-2
 Depends: methods, stats, rARPACK, Matrix, CompQuadForm
 NeedsCompilation: no
 Encoding: UTF-8
-RoxygenNote: 6.1.1
+RoxygenNote: 7.2.1
 Collate: 'A_Kernel.R' 'A_BurdenKernel.R' 'A_LinearKernel.R'
         'A_PolyKernel.R' 'B_PvMethod.R' 'B_PvMethod_Davies.R'
         'B_PvMethod_Liu.R' 'C_BinomialTrait.R' 'C_GaussianTrait.R'
         'D_NullResult.R' 'calcLocalKernel.R' 'distanceMatrix.R'
         'mainCode.R' 'point.R' 'pvResamp.R'
-Packaged: 2022-06-05 18:59:46 UTC; 19194
+Packaged: 2023-10-01 17:33:27 UTC; 19194
 Repository: CRAN
-Date/Publication: 2022-06-06 23:10:27 UTC
+Date/Publication: 2023-10-01 18:00:02 UTC

MD5

@@ -1,5 +1,6 @@
-1e3f3132851ad86bcd55e39bf6bc9822 *DESCRIPTION
+f1ba4020271a14e4f1470738ed665dc0 *DESCRIPTION
 79cb6e589daecdb2d8cc911fdc698376 *NAMESPACE
+95f49148ef924801b2279973dd785fd7 *NEWS
 45336051ca2c9ed46420e69b6a1da121 *R/A_BurdenKernel.R
 2bc358a06faf5e6b01abd2a6021afbdf *R/A_Kernel.R
 beae441800c9af958eb05ee122b4f378 *R/A_LinearKernel.R
@@ -13,7 +14,6 @@ d5c8e2daad26f58f5752588f0cad2d7c *R/C_GaussianTrait.R
 89816a3d348fa392795b5943166b6ceb *R/calcLocalKernel.R
 a9ae895b837fb3f48a1e2fd85d9617ab *R/distanceMatrix.R
 a248891360e94609fa98ab448b3f5f84 *R/mainCode.R
-4a9f6833452e57edd307fdc0ad988da2 *R/point.R
+ec510af1ca405a5c06b3234c0680acc4 *R/point.R
 150be2a9e63790cb936423ec136745ab *R/pvResamp.R
-e2a05623cc5c4965177e237414c4becc *man/POINT-package.Rd
-3f6fae015984ab4facf087043cb622eb *man/point.Rd
+e052ed18efe26f5fb897572ef9e12235 *man/point.Rd

NEWS

@@ -0,0 +1,11 @@
+POINT v1.3 (Release date: 2023-10-01)
+
+Changes:
+
+* Cleaned-up documentation; removed package.Rd file
+
+POINT v1.2 (Release date: 2022-06-06)
+
+Changes:
+
+* Maintainer e-mail address

R/point.R

@@ -68,7 +68,7 @@
 #'
 #'   #no non-genetic covariates
 #'   X <- NULL
-#'   mu <- -0.05 + snp \%*\% betaG
+#'   mu <- -0.05 + snp %*% betaG
 #'
 #'   pryy <- exp(mu)/(1+exp(mu))
 #'   yy <- sapply(X = pryy, FUN = stats::rbinom, n = 1, size = 1)