Package 'RFlocalfdr.data'

Title: Data for the Vignette and Examples in 'RFlocalfdr'
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>.
Authors: Robert Dunne [aut, cre]
Maintainer: Robert Dunne <[email protected]>
License: GPL (>= 3)
Version: 0.0.3
Built: 2026-05-28 10:36:03 UTC
Source: https://github.com/cran/RFlocalfdr.data

Help Index

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"

...

Source

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE994