@@ -36,7 +36,7 @@ Suggests:

 LinkingTo: Rcpp, flowWorkspace, BH(>= 1.62.0-1), RProtoBufLib

 VignetteBuilder: knitr

 SystemRequirements: xml2, GNU make, C++11

-RoxygenNote: 5.0.1

+RoxygenNote: 6.0.1

 Collate:

     'GatingSet2cytobank.R'

     'GatingSet2flowJo.R'

@@ -50,4 +50,3 @@ GatingSet2cytobank(gs, outFile) #type by default is 'cytobank'

 }

-

@@ -32,4 +32,3 @@ GatingSet2flowJo(gs, outFile)

 }

-

@@ -25,4 +25,3 @@ XML root node

 \description{

 add customInfo nodes to each gate node and add BooleanAndGates

 }

-

@@ -30,4 +30,3 @@ dt_merged <- compare.counts(gs, statsfile, id.vars = "population")

 all.equal(dt_merged[, count.x], dt_merged[, count.y], tol = 5e-4)

 }

-

@@ -20,4 +20,3 @@ compensated GatingSet

 \description{

 compensate a GatingSet based on the compensation information stored in graphGML object

 }

-

@@ -17,4 +17,3 @@ a graphNEL represent the population tree. The gate and population name are store

 \description{

 Reconstruct the population tree from the GateSets

 }

-

@@ -25,4 +25,3 @@ gs <- cytobank2GatingSet(xmlfile, fcsFiles)

 #plotGate(gs[[1]])

 }

-

@@ -3,10 +3,10 @@

 \docType{class}

 \name{divaWorkspace-class}

 \alias{divaWorkspace-class}

-\alias{getSampleGroups,divaWorkspace-method}

 \alias{getSamples,divaWorkspace-method}

-\alias{parseWorkspace,divaWorkspace-method}

+\alias{getSampleGroups,divaWorkspace-method}

 \alias{show,divaWorkspace-method}

+\alias{parseWorkspace,divaWorkspace-method}

 \title{divaWorkspace class

 Inherited from \link{flowJoWorkspace-class}}

 \usage{

@@ -22,4 +22,3 @@ Inherited from \link{flowJoWorkspace-class}}

 divaWorkspace class

 Inherited from \link{flowJoWorkspace-class}

 }

-

@@ -2,9 +2,9 @@

 % Please edit documentation in R/read.gatingML.cytobank.R

 \name{extend}

 \alias{extend}

-\alias{extend.ellipsoidGate}

 \alias{extend.polygonGate}

 \alias{extend.rectangleGate}

+\alias{extend.ellipsoidGate}

 \title{extend the gate to the minimum and maximum limit of both dimensions based on the bounding information.}

 \usage{

 extend(gate, bound, data.range = NULL, plot = FALSE,

@@ -56,4 +56,3 @@ bound <- matrix(c(100,3e3,100,3e3), byrow = TRUE, nrow = 2, dimnames = list(c("F

 bound

 pg.extened <- extend(pg, bound, plot = TRUE)

 }

-

@@ -20,4 +20,3 @@ Nothing. As the side effect, gates generated by gating methods are saved in \cod

 \description{

 It applies the gates to the GatingSet based on the population tree described in graphGML.

 }

-

@@ -24,4 +24,3 @@ g <- read.gatingML.cytobank(xmlfile)

 getChildren(g, "GateSet_722326")

 getParent(g, "GateSet_722326")

 }

-

@@ -16,4 +16,3 @@ compensation object or "FCS" when compensation comes from FCS keywords

 \description{

 Extract compensation from graphGML object.

 }

-

@@ -18,4 +18,3 @@ the gate information associated with the node

 \description{

 get gate from the node

 }

-

@@ -29,4 +29,3 @@ g <- read.gatingML.cytobank(xmlfile)

 getNodes(g)

 getNodes(g, only.names = FALSE)

 }

-

@@ -18,4 +18,3 @@ a graphNEL node

 \description{

 get parent nodes

 }

-

@@ -16,4 +16,3 @@ transformerList object

 \description{

 Extract transformations from graphGML object.

 }

-

@@ -11,4 +11,3 @@ associated with each node as nodeData. Compensation and transformations are stor

 \details{

 The class simply extends the graphNEL class and exists for the purpose of method dispatching.

 }

-

@@ -19,4 +19,3 @@ TRUE if path is found, FALSE if not path is matched.

 \description{

 Given the leaf node, try to find out if a collection of nodes can be matched to a path in a graph(tree) by the bottom-up searching

 }

-

@@ -33,4 +33,3 @@ getNodes(gs)

 plotGate(gs[[1]])

 }

 }

-

@@ -18,4 +18,3 @@ a data.frame that contains three columns: id (gateId), name (gate name), fcs (fc

 Fcs filename and gate name stored in 'custom_info' element are beyong the scope of

 the gatingML standard and thus not covered by the default 'read.gatingML'.

 }

-

@@ -27,4 +27,3 @@ g <- read.gatingML.cytobank(xmlfile)

 plot(g)

 }

-

@@ -25,4 +25,3 @@ xml <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML")

 g <- read.gatingML.cytobank(xml) #parse the population tree

 #plot(g) #visualize it

 }

-

@@ -21,4 +21,3 @@ It is for internal use by the diva parser

 set.count.xml(gh, "CD3", 10000)

 }

 }

-

@@ -16,4 +16,3 @@ nothing

 \description{

 show method for graphGML

 }

-