GM-CSF censored data set in the cg package

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Description

A data frame used to illustrate the cg package. It has a One Factor / One-Way / Unpaired Samples layout. It also contains left-censored values of varying degree in each of the six groups. There are three equivalent data frame versions documented here.

Usage

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Format

A 45 row data frame with up to 8 observations per group from an experiment on the following 6 groups.

PBS/Tg 197

phosphate buffered saline control group

1mg/kg/Tg 197

1 mg/kg dose

3mg/kg/Tg 197

3 mg/kg dose

10/mg/kg/Tg 197

10 mg/kg dose

30/mg/kg/Tg 197

30 mg/kg dose

PBS/WT

phosphate buffered saline control group of wild-type mice

The first five groups have transgenic (Tg197) mice subjects, a well established model to induce arthritis. The sixth group are "wild-type" mice that did not have arthritis induced. The various doses of the inner four groups are administrations of golimumab, a monoclonal antibody therapy.

There can be either 2, 3, or 4 columns in the data frame. The above 6 items are the levels of the first column's factor, named grp.

2 columns

The data frame name is gmcsfcens.listfmt1. The second column endpt contains the character observations that can represent complete observations, and also left- or right-censored ones, in the same way that gmcsfcens does.

3 columns

The data frame name is gmcsfcens.listfmt2. The second column endpt contains numeric observations, and the third column status indicates whether the observation is complete/not censored (1), and 0 if left-censored. See prepareCGOneFactorData for the explanation of why the value of 0 and not 2 is required. In the example code below, the leftcensor=TRUE argument needs to be specified when this format version is used.

4 columns

The data frame name is gmcsfcens.listfmt3. The second and third columns endpt1 and endpt2 contain numeric observations, and the fourth column status indicates whether the observation is complete/not censored (1), and 2 if left-censored. See prepareCGOneFactorData for the explanation of this format, and the example code below.

Details

The gmcsfcens.listfmt* data sets that comes with the cg package are in a "listed" format, detailed below.

The 6 groups are regarded as levels of one factor in the prepareCGOneFactorData, fit, and other methods in the cg package.

The gmcsfcens.listfmt data sets are alternative formats of the gmcsfcens data set. See that help file for details. Once a gmcsfcens.listfmt data set is prepared into a cgOneFactorData object, all the subsequent methods work on the object in the same way.

GM-CSF stands for Granulocyte macrophage colony stimulating factor, a type of cytokine that is important in the growth of white blood cells. It is one of the outcomes measured in the experiment described in the references section below. Therapeutic inhibition of it may be beneficial in cases where too many white blood cells are produced, such as arthritis. In other situations where white blood cell counts are low, stimulation of it is desired. In the referenced study below, GM-CSF is evaluated in the context of inflammation.

Note

Contact cg@billpikounis.net for bug reports, questions, concerns, and comments.

References

Shealy, D., Cai, A., Staquet, K., Baker, A., Lacy, E., Johns, L., Vafa, O., Gunn, G., Tam, S., Sague, S., Wang, D., Brigham-Burke, M., Dalmonte, P., Emmell, E., Pikounis, B., Bugelski, P., Zhou, H., Scallon, B., Giles-Komar, J. (2010). "Characterization of Golimumab (CNTO148), a human monoclonal antibody specific for human tumor necrosis factor ", mAbs, Volume 2, Issue 4, 428-439.

See Also

gmcsfcens, prepareCGOneFactorData

Examples

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data(gmcsfcens.listfmt1)
str(gmcsfcens.listfmt1)

data(gmcsfcens.listfmt2)
str(gmcsfcens.listfmt2)

data(gmcsfcens.listfmt3)
str(gmcsfcens.listfmt3)

## Analogous to prepareCGOneFactorData call on gmcsfcens data frame format,
##  subsequent methods will work for gmcsfcens.listfmt.data objects below:

## leftcensor argument can be left as default NULL
gmcsfcens.listfmt1.data <- prepareCGOneFactorData(gmcsfcens.listfmt1, format="listed",
                                                  analysisname="cytokine",
                                                  endptname="GM-CSF (pg/ml)",
                                                  logscale=TRUE)

## leftcensor=TRUE argument needs to be set
gmcsfcens.listfmt2.data <- prepareCGOneFactorData(gmcsfcens.listfmt2, format="listed",
                                                  analysisname="cytokine",
                                                  endptname="GM-CSF (pg/ml)",
                                                  logscale=TRUE,
                                                  leftcensor=TRUE)

## leftcensor argument can be left as default NULL
gmcsfcens.listfmt3.data <- prepareCGOneFactorData(gmcsfcens.listfmt3, format="listed",
                                                  analysisname="cytokine",
                                                  endptname="GM-CSF (pg/ml)",
                                                  logscale=TRUE)
## as they do on gmcsfcens.data:

gmcsfcens.data <- prepareCGOneFactorData(gmcsfcens, format="groupcolumns",
                                         analysisname="cytokine",
                                         endptname="GM-CSF (pg/ml)",
                                         logscale=TRUE)

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