Description Usage Format Source References Examples
The data result from two experiments investigating the expression response of human T cells to PMA and ionomicin treatment.
The first data set (tcell.34
) contains the temporal expression levels of 58 genes
for 10 unequally spaced time points. At each time point there are 34
separate measurements. The second data set (tcell.10
) stems from
a related experiment considering
the same genes and identical time points, and contains
10 further measurements per time point. See Rangel et al. (2004) for more details.
1 |
tcell.10
and tcell.34
are longitudinal
objects,
i.e. matrices with 58 colums each and a number of extra attributes
(see longitudinal
and longitudinal.util
).
The vector tcell.gene.descriptions
contains the
description of the functions of the 58 investigated genes.
This data is described in Rangel et al. (2004).
Rangel, C., Angus, J., Ghahramani, Z., Lioumi, M., Sotheran, E., Gaiba, A., Wild, D. L., and Falciani, F. (2004) Modeling T-cell activation using gene expression profiling and state-space models. Bioinformatics, 20, 1361–1372.
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 29 30 31 32 | # load "longitudinal" library
library("longitudinal")
# load data sets
data(tcell)
# data set with 10 repeats
dim(tcell.10)
summary(tcell.10)
is.longitudinal(tcell.10)
is.regularly.sampled(tcell.10)
is.equally.spaced(tcell.10)
get.time.repeats(tcell.10)
# data set with 34 repeats
dim(tcell.34)
summary(tcell.34)
is.longitudinal(tcell.34)
is.regularly.sampled(tcell.34)
is.equally.spaced(tcell.34)
get.time.repeats(tcell.34)
# descriptions of the first nine genes
tcell.gene.description[1:9]
# plot the first nine time series
plot(tcell.10, 1:9)
plot(tcell.34, 1:9)
# Rangel et al. use the combined data set
tcell.44 <- combine.longitudinal(tcell.34, tcell.10)
plot(tcell.44, 1:9)
|
Loading required package: corpcor
[1] 100 58
Longitudinal data:
58 variables measured at 10 different time points
Total number of measurements per variable: 100
Repeated measurements: yes
To obtain the measurement design call 'get.time.repeats()'.
[1] TRUE
[1] TRUE
[1] FALSE
$time
[1] 0 2 4 6 8 18 24 32 48 72
$repeats
[1] 10 10 10 10 10 10 10 10 10 10
[1] 340 58
Longitudinal data:
58 variables measured at 10 different time points
Total number of measurements per variable: 340
Repeated measurements: yes
To obtain the measurement design call 'get.time.repeats()'.
[1] TRUE
[1] TRUE
[1] FALSE
$time
[1] 0 2 4 6 8 18 24 32 48 72
$repeats
[1] 34 34 34 34 34 34 34 34 34 34
[1] "retinoblastoma 1 (including osteosarcoma)"
[2] "cyclin G1"
[3] "TNF receptor-associated factor 5"
[4] "clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"
[5] "mitogen-activated protein kinase 9"
[6] "CD27-binding (Siva) protein"
[7] "CD69 antigen (p60, early T-cell activation antigen)"
[8] "zinc finger protein, subfamily 1A, 1 (Ikaros)"
[9] "interleukin 4 receptor"
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