Description Usage Format Examples
A data set used by De Vito et al. (2019) as an illustrative example.
1 |
A list of two matrices, each with 63 columns and 285 and 140 rows, respectively.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | ## Not run:
The commands below show how the dataset was obtained from libraries on the Bioconductor repository.
source("http://bioconductor.org/biocLite.R")
biocLite(c("limma", "curatedOvarianData", "RTCGAToolbox"), suppressUpdates=TRUE)
library(curatedOvarianData)
library(RTCGAToolbox)
data(package="curatedOvarianData")
data(GSE20565_eset)
data(GSE9891_eset)
im_response <- c(
"TP53",
"TUBA3C","PRKACG","FGF6","FGF23","FGF22","FGF20","ASB4","TUBB1","LAT","ULBP1","NCR1",
"SIGLEC5","CD160","KLRD1","NCR3","TRIM9","FGF18","ICOSLG",
"MYH2","C9","MBL2",
"GRIN2B","POLR2F","CSF2","IL5","CRP","C8A","SPTA1","GRIN2A","CCR6","FGA","LBP",
"DUSP9","FCN2","PRKCG","ADCY8","IL5RA","GRIN1","C8B",
"GH2","TNFSF18","GRIN2D","FGB","PRL","SPTBN5","CD70","FGG","RASGRF1","IFNG",
"SPTBN4","TRIM10","ACTN2","LTA","TNFSF11","GRIN2C","CAMK2B","SPTB","IL1A","TNFRSF13B",
"ITGA2B","CAMK2A","TRIM31","EREG")
GSE20_eset <- t(as.matrix(GSE20565_eset))
GSE98_eset <- t(as.matrix(GSE9891_eset))
leD <- length(im_response)
mat1 <- matrix(sapply(1:leD, function(i) which(colnames(GSE20_eset)==im_response[i])))
mat2 <- matrix(sapply(1:leD, function(i) which(colnames(GSE98_eset)==im_response[i])))
GSE20 <- matrix(c(GSE20_eset[,mat1]), 140, leD)
GSE98 <-matrix(c(GSE98_eset[,mat2]), 285, leD)
data_immune <- list(GSE98, GSE20)
## End(Not run)
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