vcaplong: Long-format data of the Castration-resistant Prostate Cancer...

In hamlet: Hierarchical Optimal Matching and Machine Learning Toolbox

Description

The long-format of the VCaP experiment PSA-measurements may be used to model longitudinal measurements during interventions (Vehicle, ARN, or MDV). Body weights and PSA were measured weekly during the experiment. PSA concentrations were log2-transformed to make data better normally distributed.

Usage

data(vcaplong)

Format

A data frame with 225 observations on the following 11 variables.

PSA

Raw PSA (prostate-specific antigen) measurements with unit (ug/l)

log2PSA

Log2-transformed PSA (prostate-specific antigen) measurements with unit (log2 ug/l)

BW

Body weights (g)

Submatch

A grouping factor for indicating which measurements belong to individuals that were part of the same submatch prior to interventions

ID

A character vector indicating unique animal IDs

Week

Week of the experiment, notice that this is not the same as the week of drug administration (see below)

DrugWeek

Week since beginning administration of the drugs

Group

Grouping factor for intervention groups of the observations

Vehicle

Binary indicator for which observations belonged to the group 'Vehicle'

ARN

Binary indicator for which observations belonged to the group 'ARN-509'

MDV

Binary indicator for which observations belonged to the group 'MDV3100'

Details

Notice that the long-format is suitable for modeling longitudinal measurements. The grouping factors ID or Submatch could be used to group observations belonging to a single individual or matched individuals.

Source

Laajala TD, Jumppanen M, Huhtaniemi R, Fey V, Kaur A, et al. (2016) Optimized design and analysis of preclinical intervention studies in vivo. Sci Rep. 2016 Aug 2;6:30723. doi: 10.1038/srep30723.

Knuuttila M, Yatkin E, Kallio J, Savolainen S, Laajala TD, et al. (2014) Castration induces upregulation of intratumoral androgen biosynthesis and androgen receptor expression in orthotopic VCaP human prostate cancer xenograft model. Am J Pathol. 2014 Aug;184(8):2163-73. doi: 10.1016/j.ajpath.2014.04.010.

Examples

data(vcaplong)

str(vcaplong)
head(vcaplong)

library(lattice)
xyplot(log2PSA ~ DrugWeek | Group, data = vcaplong, type="l", group=ID, layout=c(3,1))
xyplot(BW ~ DrugWeek | Group, data = vcaplong, type="l", group=ID, layout=c(3,1))

Example output

'data.frame':	225 obs. of  11 variables:
 $ PSA     : num  21.3 45.7 54.5 53.5 27.6 ...
 $ log2PSA : num  4.41 5.51 5.77 5.74 4.79 ...
 $ BW      : num  35 36.1 37.9 37.5 39.7 31.6 31.7 32.4 33.5 33.3 ...
 $ Submatch: chr  "Submatch_1" "Submatch_1" "Submatch_1" "Submatch_1" ...
 $ ID      : chr  "ID003" "ID003" "ID003" "ID003" ...
 $ Week    : int  10 11 12 13 14 10 11 12 13 14 ...
 $ DrugWeek: int  0 1 2 3 4 0 1 2 3 4 ...
 $ Group   : chr  "Vehicle" "Vehicle" "Vehicle" "Vehicle" ...
 $ Vehicle : num  1 1 1 1 1 0 0 0 0 0 ...
 $ ARN     : int  0 0 0 0 0 0 0 0 0 0 ...
 $ MDV     : int  0 0 0 0 0 1 1 1 1 1 ...
     PSA  log2PSA   BW    Submatch    ID Week DrugWeek   Group Vehicle ARN MDV
11 21.30 4.412782 35.0  Submatch_1 ID003   10        0 Vehicle       1   0   0
12 45.69 5.513807 36.1  Submatch_1 ID003   11        1 Vehicle       1   0   0
13 54.50 5.768184 37.9  Submatch_1 ID003   12        2 Vehicle       1   0   0
14 53.55 5.742815 37.5  Submatch_1 ID003   13        3 Vehicle       1   0   0
15 27.64 4.788686 39.7  Submatch_1 ID003   14        4 Vehicle       1   0   0
41  7.55 2.916477 31.6 Submatch_10 ID007   10        0     MDV       0   0   1

hamlet documentation built on May 1, 2019, 8:40 p.m.