add methods is to the importFrom

.gitignore

@@ -4,5 +4,7 @@
 .Ruserdata
 .DS_Store
 *.Rproj
+.o
+.dll
 doc
 Meta

DESCRIPTION

@@ -8,7 +8,7 @@ Imports: R2jags, abind, cowplot, grid, forcats, stringr,
          BSgenome.Hsapiens.UCSC.hg19, BiocGenerics, tidyr, grDevices, stats,
          TxDb.Hsapiens.UCSC.hg19.knownGene, utils, methods, Rcpp
 Suggests: knitr, rmarkdown, testthat, BiocStyle
-Version: 0.99.3
+Version: 0.99.4
 Date: 2019-06-05
 Authors@R: c(person("Zhi", "Yang", email = "zyang895@gmail.com", 
              role = c("aut", "cre")),

NAMESPACE

@@ -24,6 +24,7 @@ importFrom(forcats,fct_relevel)
 importFrom(forcats,fct_reorder)
 importFrom(grDevices,hcl)
 importFrom(grid,unit.c)
+importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,slot)
 importFrom(stats,aggregate)

NEWS

@@ -7,3 +7,5 @@ Changes in version 0.99.2 (2019-06-05)
 Changes in version 0.99.3 (2019-06-21)
 + Fix the issues commented by the Bioconductor reviewer
 
+Changes in version 0.99.4 (2019-06-22)
++ Remove git tracking .o and .dll files

R/hilda_diagnosis.R

@@ -6,6 +6,8 @@
 #'
 #' @return a number for the Rhat statistic.
 #'
+#' @importFrom methods is
+#' 
 #' @examples
 #' 
 #' inputFile <- system.file("extdata/hildaLocal.rdata", package="HiLDA")
@@ -16,7 +18,7 @@
 #
 
 hildaRhat <- function(jagsOutput) {
-    if(class(jagsOutput) != "rjags") {
+    if(is(jagsOutput) != "rjags") {
         stop("Not an output object from running the HiLDA tests.")
     }
     return(max(jagsOutput$BUGSoutput$summary[, "Rhat"]))
@@ -29,6 +31,8 @@ hildaRhat <- function(jagsOutput) {
 #' @param jagsOutput the output jags file generated by the jags function from
 #' the R2jags package.
 #'
+#' @importFrom methods is
+#'
 #' @examples
 #' 
 #' inputFile <- system.file("extdata/hildaLocal.rdata", package="HiLDA")
@@ -42,7 +46,7 @@ hildaRhat <- function(jagsOutput) {
 #
 
 hildaLocalResult <- function(jagsOutput) {
-    if(class(jagsOutput) != "rjags") {
+    if(is(jagsOutput) != "rjags") {
         stop("Not an output object from running the HiLDA tests.")
     }
     rownames <- rownames(jagsOutput$BUGSoutput$summary)
@@ -57,6 +61,8 @@ hildaLocalResult <- function(jagsOutput) {
 #' @param pM1 the probability of sampling the null (default: 0.5)
 #' @return a number for the Bayes factor
 #'
+#' @importFrom methods is
+#'
 #' @examples
 #' 
 #' load(system.file("extdata/sample.rdata", package="HiLDA"))
@@ -68,7 +74,7 @@ hildaLocalResult <- function(jagsOutput) {
 #
 
 hildaGlobalResult <- function(jagsOutput, pM1=0.5) {
-    if(class(jagsOutput) != "rjags") {
+    if(is(jagsOutput) != "rjags") {
         stop("Not an output object from running the HiLDA tests.")
     }
 

R/hilda_plot.R

@@ -13,11 +13,12 @@
 #' hildaPlotSignature(hildaLocal)
 #'
 #' @importFrom cowplot plot_grid
+#' @importFrom methods is
 #' @export
 
 hildaPlotSignature <- function(hildaResult, sigOrder=NULL, colorList = NULL,
                                ...) {
-    if(class(hildaResult) != "rjags") {
+    if(is(hildaResult) != "rjags") {
         stop("Not an output object from running the HiLDA tests.")
     }
 
@@ -110,6 +111,7 @@ hildaPlotSignature <- function(hildaResult, sigOrder=NULL, colorList = NULL,
 #' @importFrom grid unit.c
 #' @importFrom forcats fct_relevel fct_reorder
 #' @importFrom stats aggregate
+#' @importFrom methods is
 #' @export
 
 
@@ -118,11 +120,11 @@ hildaBarplot <- function(inputG, hildaResult, sigOrder=NULL, refGroup,
                          charSize=3) {
     numSig <- dim(hildaResult$BUGSoutput$mean$pStates1)[3]
 
-    if(class(inputG) != "MutationFeatureData") {
+    if(is(inputG)[1] != "MutationFeatureData") {
         stop("Not an output object from reading in the data using HiLDA.")
     }
 
-    if(class(hildaResult) != "rjags") {
+    if(is(hildaResult) != "rjags") {
         stop("Not an output object from running the HiLDA tests.")
     }
 
@@ -205,6 +207,7 @@ hildaBarplot <- function(inputG, hildaResult, sigOrder=NULL, refGroup,
 #' @importFrom cowplot plot_grid
 #' @importFrom grid unit.c
 #' @import ggplot2
+#' @importFrom methods is
 #'
 #' @export
 
@@ -216,11 +219,11 @@ hildaDiffPlot <- function(inputG, hildaResult, sigOrder=NULL, charSize=3) {
         sigOrder <- seq_len(numSig)
     }
 
-    if(class(inputG) != "MutationFeatureData") {
+    if(is(inputG)[1] != "MutationFeatureData") {
         stop("Not an output object from reading in the data using HiLDA.")
     }
 
-    if(class(hildaResult) != "rjags") {
+    if(is(hildaResult) != "rjags") {
         stop("Not an output object from running the HiLDA tests.")
     }
 

R/hilda_test.R

@@ -28,6 +28,7 @@
 #' @importFrom R2jags jags
 #' @importFrom abind abind
 #' @importFrom stats reshape
+#' @importFrom methods is
 #' @export
 
 hildaTest <- function(inputG, numSig, refGroup, useInits=NULL, sigOrder=NULL, 
@@ -44,6 +45,10 @@ hildaTest <- function(inputG, numSig, refGroup, useInits=NULL, sigOrder=NULL,
         stop(paste("There are more reference samples than the total samples"))
     }
 
+    if(is(inputG)[1] != "MutationFeatureData") {
+        stop("Not an output object from reading in the data using HiLDA.")
+    }
+
     # reshape the counts of input data
     countWide <- as.data.frame(t(inputG@countData))
     colnames(countWide) <- c("type", "sample", "count")

R/pm_getSignature.R

@@ -24,12 +24,12 @@
 #' @useDynLib HiLDA
 #' @importFrom Rcpp sourceCpp
 #' @importFrom stats rgamma
-#' @importFrom methods slot
+#' @importFrom methods slot is
 #' @export
 pmgetSignature <- function(mutationFeatureData, K, numInit = 10, tol = 1e-4, 
                            maxIter = 10000) {
 
-    if (class(mutationFeatureData) != "MutationFeatureData") {
+    if (is(mutationFeatureData)[1] != "MutationFeatureData") {
       stop("This inputfile is not an MutationFeatureData object.")
     }
 

R/pm_plot.R

@@ -14,6 +14,7 @@
 #'
 #' @importFrom cowplot plot_grid
 #' @importFrom grDevices hcl
+#' @importFrom methods is
 #' @export
 
 pmPlotSignature <- function(inputParam, sigOrder=NULL, colorList=NULL, ...) {
@@ -24,7 +25,7 @@ pmPlotSignature <- function(inputParam, sigOrder=NULL, colorList=NULL, ...) {
         sigOrder <- seq_len(numSig)
     }
 
-    if (class(inputParam) != "EstimatedParameters") {
+    if (is(inputParam)[1] != "EstimatedParameters") {
         stop("The inputParam object is not an EstimatedParameters object")
     }
 
@@ -78,6 +79,7 @@ pmPlotSignature <- function(inputParam, sigOrder=NULL, colorList=NULL, ...) {
 #' @importFrom tidyr gather_
 #' @importFrom grid unit.c
 #' @importFrom forcats fct_relevel fct_reorder
+#' @importFrom methods is
 #' @export
 
 pmBarplot <- function(inputG, inputParam, sigOrder=NULL, refGroup=NULL,
@@ -89,11 +91,11 @@ pmBarplot <- function(inputG, inputParam, sigOrder=NULL, refGroup=NULL,
         sigOrder <- seq_len(numSig)
     }
 
-    if (class(inputParam) != "EstimatedParameters") {
+    if (is(inputParam)[1] != "EstimatedParameters") {
         stop("The inputParam object is not an EstimatedParameters object")
     }
 
-    if(class(inputG) != "MutationFeatureData") {
+    if(is(inputG)[1] != "MutationFeatureData") {
         stop("Not an output object from reading in the data using HiLDA.")
     }
 
@@ -191,6 +193,7 @@ pmBarplot <- function(inputG, inputParam, sigOrder=NULL, refGroup=NULL,
 #' @importFrom tidyr gather_
 #' @importFrom grid unit.c
 #' @importFrom forcats fct_relevel fct_reorder
+#' @importFrom methods is
 #' @export
 
 pmMultiBarplot <- function(inputG, inputParam, sigOrder=NULL, groupIndices,
@@ -201,11 +204,11 @@ pmMultiBarplot <- function(inputG, inputParam, sigOrder=NULL, groupIndices,
         sigOrder <- seq_len(numSig)
     }
 
-    if(class(inputG) != "MutationFeatureData") {
+    if(is(inputG)[1] != "MutationFeatureData") {
         stop("Not an output object from reading in the data using HiLDA.")
     }
 
-    if (class(inputParam) != "EstimatedParameters") {
+    if (is(inputParam)[1] != "EstimatedParameters") {
         stop("The inputParam object is not an EstimatedParameters object")
     }