| Title: | Data for the Vignette and Examples in 'RFlocalfdr' |
| Version: | 0.0.3 |
| Description: | Data for the vignette and examples in 'RFlocalfdr'. Contains a dataset of 1103547 importance values, and the table of variables used in the random forest splits. The data is Chromosome 22 taken from Auton et al. (2015) <doi:10.1038/nature15393>. It also contains a 51 samples by 22283 genes data set taken from Spira et al. (2004) <doi:10.1165/rcmb.2004-0273OC>. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Depends: | R (≥ 2.10) |
| LazyDataCompression: | xz |
| LazyData: | true |
| NeedsCompilation: | no |
| Packaged: | 2023-10-27 09:03:52 UTC; dun280 |
| Author: | Robert Dunne 
[aut, cre] |
| Maintainer: | Robert Dunne <rob.dunne@csiro.au> |
| Repository: | CRAN |
| Date/Publication: | 2023-10-27 10:30:02 UTC |
ch22 importance values
Description
A dataset containing 1103547 importance values, and a table of variables used in splits. Note that the importances have not been logged.
Usage
ch22
Format
A list
- imp
importaces
- C
table of counts
Source
A Global Reference for Human Genetic Variation, Auton et al., Nature, 2015, 526:7571 pp 68–74
Examples
## Not run:
library(ranger)
system.time(fit.ranger.7 <- ranger(dependent.variable.name= "V1", data = aa2,
importance = "impurity",
num.threads=20,num.trees = 100000,
seed=123))
#Ranger result
#Call:
#ranger(dependent.variable.name = "V1", data = aa2, importance = "impurity",
# num.threads = 20, num.trees = 1e+05, seed = 123)
#Type: Classification
#Number of trees: 1e+05
#Sample size: 2504
#Number of independent variables: 1103547
#Mtry: 1050
#Target node size: 1
#Variable importance mode: impurity
#Splitrule: gini
#OOB prediction error: 4.27 %
C <-count_variables(fit.ranger.7)
imp<-rf1$variable.importance
ch22<-list(imp,C)
names(ch22)<-c("imp","C")
## End(Not run)
data(ch22)
Effects of cigarette smoke on the human airway epithelial cell transcriptome
Description
A dataset containing normalized transcript measurements for 51 subjects and 22283 transcripts. See Spira et al (2004). "Gene Expression Profiling of Human Lung Tissue from Smokers with Severe Emphysema", Am J Respir Cell Mol Biol.
Usage
smoking
Format
A list with rma (the transcript data) and y (the class labels):
- rma
51 by 22283, log2 real values
- y
a character vector, "smoking" and "never-smoked"
...