Merge pull request #613 from adeschen/main

Update default parameter in snpgdsIBDKING() function and adjust unit test

Author: adeschen

.github/workflows/check-bioc.yaml

@@ -52,11 +52,12 @@ jobs:
       matrix:
         config:
          ##- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
-         - { os: ubuntu-latest, r: '4.4.1', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
-         ## - { os: macOS-latest, r: '4.4', bioc: '3.19'}
-         - { os: macOS-latest, r: '4.4.1', bioc: '3.20'}
+         - { os: ubuntu-latest, r: '4.5.0', bioc: '3.21', cont: "bioconductor/bioconductor_docker:RELEASE_3_21", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
+         - { os: ubuntu-devel, r: '4.6.0', bioc: '3.22', cont: "bioconductor/bioconductor_docker:RELEASE_3_22", rspm: "https://packagemanager.posit.co/cran/__linux__/jammy/latest" }
+        ## - { os: macOS-latest, r: '4.4', bioc: '3.19'}
+         - { os: macOS-latest, r: '4.5.0', bioc: '3.21'}
          ## - { os: windows-latest, r: '4.2.2', bioc: '3.16'}
-         - { os: windows-latest, r: '4.4.1', bioc: '3.20'}
+         - { os: windows-latest, r: '4.5.0', bioc: '3.21'}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

R/gdsWrapper_internal.R

@@ -1095,7 +1095,7 @@ runIBDKING <- function(gds, profileID=NULL, snpID=NULL, maf=0.05, verbose) {
 
     ## Calculate IBD coefficients by KING method of moment
     ibd.robust <- snpgdsIBDKING(gdsobj=gds, sample.id=profileID,
-                        snp.id=snpID, maf=maf,
+                        snp.id=snpID, maf=maf, missing.rate=0.01,
                         type="KING-robust",
                         verbose=verbose)
 

tests/testthat/test-gdsWrapper_internal.R

@@ -132,13 +132,13 @@ test_that("runIBDKING() must return expected results", {
                                         maf=0.05, verbose=FALSE)
 
     sampleIDs <- c("NA07034", "NA07055", "NA12814")
-    ibs0 <- matrix(c(0.000000000000000, 0.079705823891870, 0.088194306191519,
-        0.079705823891870, 0.000000000000000, 0.094035785288270,
-        0.088194306191519, 0.094035785288270, 0.000000000000000), nrow=3,
+    ibs0 <- matrix(c(0.000000000000000, 0.079928243970500, 0.088100458441300,
+        0.079928243970500, 0.000000000000000, 0.093880805262109,
+        0.088100458441300, 0.093880805262109, 0.000000000000000), nrow=3,
         byrow=TRUE)
-    kinship <- matrix(c(0.500000000000000, 0.017237640936687, 0.001294777729823,
-        0.017237640936687, 0.500000000000000, -0.014341590612777,
-        0.001294777729823, -0.014341590612777, 0.500000000000000), nrow=3,
+    kinship <- matrix(c(0.500000000000000, 0.015481901439163, 0.001080847384349,
+        0.015481901439163, 0.500000000000000, -0.014173571740078,
+        0.001080847384349, -0.014173571740078, 0.500000000000000), nrow=3,
         byrow=TRUE)
 
     expect_equal(result$sample.id, sampleIDs)