sim: desease data

Description Usage Format Source See Also Examples

Description

The data set corresponds to absolute (cells/mm2) or relative (percentage of the cell type in question of the entire inflammatory cell population) densities of 5 major inflammatory cell types in synovial tissue specimens from normal human joints (“Normal”) and from patients with osteoarthritis (“OA”), non-inflammatory orthopedic arthropathies (“Orth.A”), early unclassified arthritis (“EA”), rheumatoid arthritis (“RA”), and chronic septic arthritis (“SeA”). An analysis of this data set with binary and multicategory ROC analysis has been published in Della Beffa PLOS One 2013, which also contains additional details about the data set. The dataset consists of 92 cases with 11 features and disease code.

Usage

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Format

A data.frame containing 92 observations of 11 variables.

Source

Cristina Della Beffa, Elisabeth Slansky, Claudia Pommerenke, Frank Klawonn, Jialiang Li, Lie Dai, H. Ralph Schumacher Jr., Frank Pessler (2013). The Relative Composition of the Inflammatory Infiltrate as an Additional Tool for Synovial Tissue Classification. PLoS ONE. 8(8): e72494.

See Also

dataset

Examples

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# load the dataset
data(sim)
# CD15
with(sim, by(CD15,Disease,mean))

# CD20
with(sim,tapply(CD20, Disease, FUN = mean))
with(sim, table(CD20=ifelse(CD20<=mean(CD20), "1", "2"), Disease))

Example output

Loading required package: gtools
Loading required package: Rcpp
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
Disease: Early
[1] 4.223
------------------------------------------------------------ 
Disease: Normal
[1] 0.05666667
------------------------------------------------------------ 
Disease: OA
[1] 0.5361538
------------------------------------------------------------ 
Disease: OrthArthr
[1] 0.33
------------------------------------------------------------ 
Disease: RA
[1] 6.7125
------------------------------------------------------------ 
Disease: SeA
[1] 37.66364
     Early     Normal         OA  OrthArthr         RA        SeA 
20.6700000  0.3520000  3.5526923  0.1216667 39.0195833 29.0918182 
    Disease
CD20 Early Normal OA OrthArthr RA SeA
   1     5     15 24         6 10   6
   2     5      0  2         0 14   5

HUM documentation built on May 29, 2017, 2:55 p.m.