example.setup: R data object based on example file.

In OSAT: OSAT: Optimal Sample Assignment Tool

Description

Data objects created using the example data for demonstration.

Usage

data(example.setup)

Details

See vignette for codes that created these data objects.

pheno:

a data frame created from example sample information text file.

gs:

a class gSample object created based on example sample using function setup.sample()..

gc:

a class gContainer object using function setup.container().

gSetup:

a class gExperimentSetup object. Created using optimal.shuffle() method.

gSetup2:

a class gExperimentSetup object. Created using optimal.block() method.

Examples

library("OSAT")
data(example.setup)
head(pheno)
gs
gc
gSetup

Example output

  ID SampleType     Race   AgeGrp
1  1       Case Hispanic (60,100]
2  2       Case Hispanic (60,100]
3  3       Case European (60,100]
4  4       Case European  (50,60]
5  5       Case European  (50,60]
6  6       Case European   (0,30]
An object of class "gSample"
The raw data are
  ID SampleType     Race   AgeGrp
1  1       Case Hispanic (60,100]
2  2       Case Hispanic (60,100]
3  3       Case European (60,100]
4  4       Case European  (50,60]
5  5       Case European  (50,60]
6  6       Case European   (0,30]

 ... 
     ID SampleType     Race  AgeGrp
571 571    Control European (40,50]
572 572    Control Hispanic (30,40]
573 573    Control European (30,40]
574 574    Control Hispanic (30,40]
575 575    Control European (40,50]
576 576    Control European  (0,30]

 Blocking strata in the data:

  SampleType Freq sFactor
1       Case  317       1
2    Control  259       2

 Optimization strata in the data

   SampleType     Race   AgeGrp Freq oFactor
1        Case European   (0,30]    8       1
2     Control European   (0,30]   58       2
3        Case Hispanic   (0,30]    0       3
4     Control Hispanic   (0,30]    9       4
5        Case European  (30,40]   21       5
6     Control European  (30,40]   54       6
7        Case Hispanic  (30,40]    6       7
8     Control Hispanic  (30,40]   32       8
9        Case European  (40,50]   34       9
10    Control European  (40,50]   52      10
11       Case Hispanic  (40,50]   46      11
12    Control Hispanic  (40,50]    2      12
13       Case European  (50,60]   40      13
14    Control European  (50,60]   44      14
15       Case Hispanic  (50,60]   16      15
16    Control Hispanic  (50,60]    2      16
17       Case European (60,100]   84      17
18    Control European (60,100]    6      18
19       Case Hispanic (60,100]   62      19
20    Control Hispanic (60,100]    0      20
An object of class "gContainer"

It consists of 6 IlluminaBeadChip96Plate plates.
The block level is set at plates level.
  plates cFactor Freq
1      1       1   96
2      2       2   96
3      3       3   96
4      4       4   96
5      5       5   96
6      6       6   96
The container layout is
@data$container
  plates chipRows chipColumns chips rows columns wells chipID rowID wellID
1      1        1           1     1    1       1     1      1     1      1
2      1        1           1     1    2       1     2      1     1      2
3      1        1           1     1    3       1     3      1     1      3
4      1        1           1     1    4       1     4      1     1      4
5      1        1           1     1    5       1     5      1     1      5
6      1        1           1     1    6       1     6      1     1      6
  cFactor
1       1
2       1
3       1
4       1
5       1
6       1

 ... 
    plates chipRows chipColumns chips rows columns wells chipID rowID wellID
571      6        2           4     8    1       2     7     48   286    571
572      6        2           4     8    2       2     8     48   286    572
573      6        2           4     8    3       2     9     48   286    573
574      6        2           4     8    4       2    10     48   286    574
575      6        2           4     8    5       2    11     48   286    575
576      6        2           4     8    6       2    12     48   286    576
    cFactor
571       6
572       6
573       6
574       6
575       6
576       6
An object of class "gExperimentSetup"

Number of samples in each plate by blocking strata
   
     1  2
  1 53 43
  2 53 43
  3 53 43
  4 53 43
  5 52 44
  6 53 43

Number of samples in each plate by optimization strata
   
     1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20
  1  2 12  0  2  4  6  1  7  4  7  7  0  7  9  5  0 13  0 10  0
  2  1 11  0  1  4  8  1  4  7 10 10  0  6  9  2  0 17  0  5  0
  3  1  9  0  1  2  9  1  4  4 10  6  1  5  9  2  0 23  0  9  0
  4  1  8  0  3  4 10  0  5  5  7  6  1  7  8  3  1 10  0 17  0
  5  2  8  0  0  4 12  0  5  6  9  7  0 12  5  2  1  8  4 11  0
  6  1 10  0  2  3  9  3  7  8  9 10  0  3  4  2  0 13  2 10  0

The experiment setup is
@expSetup
  ID SampleType     Race   AgeGrp plates chipRows chipColumns chips rows
1  1       Case Hispanic (60,100]      3        2           2     6    1
2  2       Case Hispanic (60,100]      3        2           3     7    2
3  3       Case European (60,100]      6        2           3     7    2
  columns wells
1       2     7
2       2     8
3       2     8

 ... 
     ID SampleType     Race  AgeGrp plates chipRows chipColumns chips rows
574 574    Control Hispanic (30,40]      1        1           1     1    1
575 575    Control European (40,50]      3        1           3     3    6
576 576    Control European  (0,30]      3        2           2     6    6
    columns wells
574       2     7
575       2    12
576       2    12

OSAT documentation built on Nov. 8, 2020, 5:48 p.m.