diff --git a/DESCRIPTION b/DESCRIPTION index b6cee5f..f8cfbac 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,24 +2,23 @@ Package: projectR Type: Package Title: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering -Version: 0.99.14 +Version: 0.99.15 Date: 2016-11-22 Author: Genevieve Stein-O'Brien Maintainer: Genevieve Stein-O'Brien Description: Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering. License: GPL (==2) Imports: - gplots (>= 2.8.0), graphics, grDevices, methods, cluster, stats, utils, - ggplot2, - reshape2, limma, - MASS + MASS, + ggplot2, + reshape2 Suggests: CoGAPS, BiocStyle, diff --git a/DESCRIPTION~ b/DESCRIPTION~ index b15241d..90f4528 100644 --- a/DESCRIPTION~ +++ b/DESCRIPTION~ @@ -2,24 +2,23 @@ Package: projectR Type: Package Title: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering -Version: 0.99.13 +Version: 0.99.14 Date: 2016-11-22 Author: Genevieve Stein-O'Brien Maintainer: Genevieve Stein-O'Brien Description: Functions for the projection of data into the spaces defined by PCA, CoGAPS, NMF, correlation, and clustering. License: GPL (==2) Imports: - gplots (>= 2.8.0), graphics, grDevices, methods, cluster, stats, utils, - ggplot2, - reshape2, limma, - MASS + MASS, + ggplot2, + reshape2 Suggests: CoGAPS, BiocStyle, diff --git a/NAMESPACE b/NAMESPACE index ca26b1c..88c38f5 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -20,7 +20,14 @@ export(geneMatchR) export(intersectoR) export(projectR) export(rotatoR) +import(MASS) +import(cluster) +import(ggplot2) +import(grDevices) import(graphics) import(limma) +import(methods) +import(reshape2) import(stats) +import(utils) importFrom(limma,lmFit) diff --git a/R/clusterPlotR.R b/R/clusterPlotR.R index 3b99ac4..ad9ccc1 100644 --- a/R/clusterPlotR.R +++ b/R/clusterPlotR.R @@ -10,6 +10,8 @@ #' @return A plot of the mean behavior for each cluster #' @export #' @import graphics +#' @import ggplot2 +#' @import reshape2 #' @examples \dontrun{ #' k.RNAseq6l3c3t<-kmeans(p.RNAseq6l3c3t,22) #' clusterPlotR(p.RNAseq6l3c3t, cls=k.RNAseq6l3c3t, NC=2,x=pd.RNAseq6l3c3t$days, col=pd.RNAseq6l3c3t$color) diff --git a/R/projectR.R b/R/projectR.R index e3b7c58..4b67fce 100644 --- a/R/projectR.R +++ b/R/projectR.R @@ -15,6 +15,9 @@ #' @import limma #' @importFrom limma lmFit #' @import stats +#' @import grDevices +#' @import methods +#' @import utils #' @export @@ -143,6 +146,7 @@ projectR.CoGAPS <- function( #' AnnotionObj=map.ESepiGen4c1l,IDcol="GeneSymbols") #' #' @import limma +#' @import cluster #' @import stats #' @export @@ -191,9 +195,10 @@ projectR.pclust <- function( #' pca.RNAseq6l3c3t<-prcomp(t(p.RNAseq6l3c3t)) #' pca.ESepiGen4c1l<-projectR(data=p.ESepiGen4c1l$mRNA.Seq,Patterns=pca.RNAseq6l3c3t, #' AnnotionObj=map.ESepiGen4c1l,IDcol="GeneSymbols") -#' +#' #' @import limma #' @import stats +#' @import MASS #' @export @@ -248,7 +253,7 @@ projectR.prcomp <- function( #' r.RNAseq6l3c3t<-rotatoR(1,1,-1,-1,pca.RNAseq6l3c3t$x[,1:2]) #' pca.ESepiGen4c1l<-projectR(data=p.ESepiGen4c1l$mRNA.Seq,Patterns=r.RNAseq6l3c3t, #' AnnotionObj=map.ESepiGen4c1l,IDcol="GeneSymbols") -#' +#' #' @import stats #' @export @@ -304,7 +309,7 @@ projectR.rotatoR <- function( #' c.RNAseq6l3c3t<-correlateR(genes="T", dat=p.RNAseq6l3c3t, threshtype="N", threshold=10, absR=TRUE) #' cor.ESepiGen4c1l<-projectR(data=p.ESepiGen4c1l$mRNA.Seq,Patterns=c.RNAseq6l3c3t,NP="PositiveCOR", #' AnnotionObj=map.ESepiGen4c1l,IDcol="GeneSymbols") -#' +#' #' @import limma #' @import stats #' @export