Lung {compound.Cox}R Documentation

Survival data for patients with non-small-cell lung cancer.

Description

A subset of the lung cancer data (Chen et al. 2007) made available by Emura et al. (2019). The subset consists of 97 gene expressions from 125 patients with non-small-cell lung cancer. The 97 genes were selected with P-value<0.20 under univariate Cox regression analyses as previously done in Emura et al. (2012) and Emura and Chen (2016). The intensity of gene expression was transformed to an ordinal level using the quantile, i.e. if the intensity of gene expression was <=25th, >25th, >50th, or >75th percentile, it was coded as 1, 2, 3, or 4, respectively (Chen et al. 2007).

Usage

data("Lung")

Format

A data frame with 125 observations on the following 100 variables.

t.vec

survival times (time to either death or censoring) in months

d.vec

censoring indicators, 1=death, 0=censoring

train

TRUE=training set, FALSE=testing set, as defined in Chen et al. (2007)

VHL

gene expression, coded as 1, 2, 3, or 4

IHPK1

gene expression, coded as 1, 2, 3, or 4

HMMR

gene expression, coded as 1, 2, 3, or 4

CMKOR1

gene expression, coded as 1, 2, 3, or 4

PLAU

gene expression, coded as 1, 2, 3, or 4

IGF2

gene expression, coded as 1, 2, 3, or 4

FGB

gene expression, coded as 1, 2, 3, or 4

MYBL2

gene expression, coded as 1, 2, 3, or 4

ODC1

gene expression, coded as 1, 2, 3, or 4

MTHFD2

gene expression, coded as 1, 2, 3, or 4

GLIPR1

gene expression, coded as 1, 2, 3, or 4

EZH2

gene expression, coded as 1, 2, 3, or 4

HCK

gene expression, coded as 1, 2, 3, or 4

CCNC

gene expression, coded as 1, 2, 3, or 4

XRCC1

gene expression, coded as 1, 2, 3, or 4

CYP1B1

gene expression, coded as 1, 2, 3, or 4

CDC25A

gene expression, coded as 1, 2, 3, or 4

CD44

gene expression, coded as 1, 2, 3, or 4

LCK

gene expression, coded as 1, 2, 3, or 4

MTHFS

gene expression, coded as 1, 2, 3, or 4

PON3

gene expression, coded as 1, 2, 3, or 4

PTPN6

gene expression, coded as 1, 2, 3, or 4

KIDINS220

gene expression, coded as 1, 2, 3, or 4

KLHL22

gene expression, coded as 1, 2, 3, or 4

RBBP6

gene expression, coded as 1, 2, 3, or 4

GABARAPL2

gene expression, coded as 1, 2, 3, or 4

SEH1L

gene expression, coded as 1, 2, 3, or 4

CITED2

gene expression, coded as 1, 2, 3, or 4

BARD1

gene expression, coded as 1, 2, 3, or 4

TLX1

gene expression, coded as 1, 2, 3, or 4

CRMP1

gene expression, coded as 1, 2, 3, or 4

CTNNA1

gene expression, coded as 1, 2, 3, or 4

ANXA5

gene expression, coded as 1, 2, 3, or 4

PTGS2

gene expression, coded as 1, 2, 3, or 4

SMC4L1

gene expression, coded as 1, 2, 3, or 4

LOC285086

gene expression, coded as 1, 2, 3, or 4

ATP11B

gene expression, coded as 1, 2, 3, or 4

CDK10

gene expression, coded as 1, 2, 3, or 4

IRF4

gene expression, coded as 1, 2, 3, or 4

MYH11

gene expression, coded as 1, 2, 3, or 4

ME3

gene expression, coded as 1, 2, 3, or 4

CCT6A

gene expression, coded as 1, 2, 3, or 4

SNCG

gene expression, coded as 1, 2, 3, or 4

MAK3

gene expression, coded as 1, 2, 3, or 4

VCPIP1

gene expression, coded as 1, 2, 3, or 4

JMJD1A

gene expression, coded as 1, 2, 3, or 4

STAT2

gene expression, coded as 1, 2, 3, or 4

DDX6

gene expression, coded as 1, 2, 3, or 4

ERBB3

gene expression, coded as 1, 2, 3, or 4

PAX2

gene expression, coded as 1, 2, 3, or 4

PCTK2

gene expression, coded as 1, 2, 3, or 4

NF1

gene expression, coded as 1, 2, 3, or 4

DLG2

gene expression, coded as 1, 2, 3, or 4

JMJD1A.1

gene expression, coded as 1, 2, 3, or 4

SUCLA2

gene expression, coded as 1, 2, 3, or 4

MMP16

gene expression, coded as 1, 2, 3, or 4

AP3B2

gene expression, coded as 1, 2, 3, or 4

HGF

gene expression, coded as 1, 2, 3, or 4

MAP2K3

gene expression, coded as 1, 2, 3, or 4

CPEB4

gene expression, coded as 1, 2, 3, or 4

ZNF264

gene expression, coded as 1, 2, 3, or 4

AXL

gene expression, coded as 1, 2, 3, or 4

CDC23

gene expression, coded as 1, 2, 3, or 4

MAST3

gene expression, coded as 1, 2, 3, or 4

COX11

gene expression, coded as 1, 2, 3, or 4

PRKAG2

gene expression, coded as 1, 2, 3, or 4

MAN1B1

gene expression, coded as 1, 2, 3, or 4

F8

gene expression, coded as 1, 2, 3, or 4

RSU1

gene expression, coded as 1, 2, 3, or 4

MMD

gene expression, coded as 1, 2, 3, or 4

AK5

gene expression, coded as 1, 2, 3, or 4

IDS

gene expression, coded as 1, 2, 3, or 4

BNIP1

gene expression, coded as 1, 2, 3, or 4

ENG

gene expression, coded as 1, 2, 3, or 4

PCDHGC3

gene expression, coded as 1, 2, 3, or 4

RALY

gene expression, coded as 1, 2, 3, or 4

WDR33

gene expression, coded as 1, 2, 3, or 4

RNF4

gene expression, coded as 1, 2, 3, or 4

PRDX1

gene expression, coded as 1, 2, 3, or 4

FXN

gene expression, coded as 1, 2, 3, or 4

PTPRU

gene expression, coded as 1, 2, 3, or 4

FRAP1

gene expression, coded as 1, 2, 3, or 4

MMP7

gene expression, coded as 1, 2, 3, or 4

CST3

gene expression, coded as 1, 2, 3, or 4

TIMP2

gene expression, coded as 1, 2, 3, or 4

TAL1

gene expression, coded as 1, 2, 3, or 4

STAT1

gene expression, coded as 1, 2, 3, or 4

CCND1

gene expression, coded as 1, 2, 3, or 4

DUSP6

gene expression, coded as 1, 2, 3, or 4

SNRPF

gene expression, coded as 1, 2, 3, or 4

MMP13

gene expression, coded as 1, 2, 3, or 4

NR2F6

gene expression, coded as 1, 2, 3, or 4

HOXA1

gene expression, coded as 1, 2, 3, or 4

RIPK1

gene expression, coded as 1, 2, 3, or 4

IL7R

gene expression, coded as 1, 2, 3, or 4

SEC13L1

gene expression, coded as 1, 2, 3, or 4

RPL5

gene expression, coded as 1, 2, 3, or 4

Details

Survival data consisting of 125 patients.

Source

Chen HY, Yu SL, Chen CH, et al (2007). A Five-gene Signature and Clinical Outcome in Non-small-cell Lung Cancer, N Engl J Med 356: 11-20.

Emura T, Matsui S, Chen HY (2019). compound.Cox: Univariate Feature Selection and Compound Covariate for Predicting Survival, Computer Methods and Programs in Biomedicine 168: 21-37.

References

Chen HY, Yu SL, Chen CH, et al (2007). A Five-gene Signature and Clinical Outcome in Non-small-cell Lung Cancer, N Engl J Med 356: 11-20.

Emura T, Matsui S, Chen HY (2019). compound.Cox: Univariate Feature Selection and Compound Covariate for Predicting Survival, Computer Methods and Programs in Biomedicine 168: 21-37.

Emura T, Chen YH (2016). Gene Selection for Survival Data Under Dependent Censoring: a Copula-based Approach, Stat Methods Med Res 25(No.6): 2840-57

Examples

data(Lung)
Lung[1:3,] ## show the first 3 samples ## 

## The five-gene signature in Chen et al. (2007) ##
temp=Lung[,"train"]==TRUE
t.vec=Lung[temp,"t.vec"]
d.vec=Lung[temp,"d.vec"]
coxph(Surv(t.vec,d.vec)~Lung[temp,"ERBB3"])
coxph(Surv(t.vec,d.vec)~Lung[temp,"LCK"])
coxph(Surv(t.vec,d.vec)~Lung[temp,"DUSP6"])
coxph(Surv(t.vec,d.vec)~Lung[temp,"STAT1"])
coxph(Surv(t.vec,d.vec)~Lung[temp,"MMD"])

[Package compound.Cox version 3.20 Index]