added fun=match.arg(fun) to roast_multi_cor

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ezlimma
 Type: Package
 Title: Streamlines and extends limma package
-Version: 0.2.5.9010
+Version: 0.2.5.9011
 Authors@R: c(person("Jonathan", "Dreyfuss", role = c("aut", "cre"), email = "[email protected]"),
              person("Hui", "Pan", role = "aut"),
 			 person("Grace", "Daher", role = "ctb"))

R/roast_multi_cor.R

@@ -23,14 +23,15 @@ roast_multi_cor <- function(object, G, pheno.tab, feat.tab, name=NA, covariates=
                     min.nfeats=3, max.nfeats=1000, alternative=c("two.sided", "less", "greater"), 
                     nrot=999, check.names=TRUE, pwy.nchar=199, seed=0){
 
+  fun <- match.arg(fun)
   stopifnot(!is.null(dim(object)), !is.null(rownames(object)), !is.null(colnames(object)), ncol(object) > 1,
             !is.null(colnames(pheno.tab)), nrow(pheno.tab) == ncol(object), limma::isNumeric(pheno.tab), colSums(!is.na(pheno.tab)) > 2,
             length(weights)!=1 || is.na(weights), length(weights)<=1 || 
               (is.numeric(weights) && all(weights>=0) && !all(is.na(weights))), 
             length(weights)<=1 || all(dim(weights)==dim(object)) || 
               length(weights)==nrow(object) || length(weights)==ncol(object),
             is.null(gene.weights) || length(gene.weights)==nrow(object),
-            is.na(name) || rownames(object) %in% rownames(feat.tab))
+            is.na(name) || all(rownames(object) %in% rownames(feat.tab)))
   if (!is.null(covariates)) stopifnot(limma::isNumeric(covariates), !is.na(covariates))
   if (check.names) stopifnot(rownames(pheno.tab)==colnames(object))
 

tests/testthat/test-roast_multi_cor.R

@@ -1,7 +1,7 @@
 des1 <- cbind(Int=1, design[, 1, drop=FALSE])
 des2 <- cbind(Int=1, design[, 1, drop=FALSE], covar=1:6)
 
-test_that("one phenotypes", {
+test_that("one phenotype", {
   # covar
   pheno.tab <- design[, 1, drop=FALSE]
   rc.des1 <- roast_cor(M, G=G, feat.tab=eztt, fun="fry", design = des1, prefix = "First3Arrays")
@@ -31,7 +31,8 @@ test_that("one phenotypes", {
 test_that("multiple pheno", {
   # NA
   mph <- data.frame(design, pheno2=pheno2)
-  expect_message(rmc.multi <- roast_multi_cor(object=M, G=G, feat.tab=eztt, pheno.tab=mph))
+  # expect_message(rmc.multi <- roast_multi_cor(object=M, G=G, feat.tab=eztt, pheno.tab=mph, name = "mph")) # to test writing to file
+  expect_message(rmc.multi <- roast_multi_cor(object=M, G=G, feat.tab=eztt, pheno.tab=mph, name = "mph"))
   rc.des1 <- roast_cor(M, G=G, feat.tab=eztt, fun="fry", design = des1, prefix = "First3Arrays")
   expect_equal(rmc.multi[, 1:6], rc.des1)
   expect_message(rc.pheno2 <- roast_cor(object=M, G=G, feat.tab=eztt, pheno=pheno2, prefix = "pheno2"))