ex_dataMatrix {sights} | R Documentation

## High-Throughput Screening example data - CMBA

### Description

An example dataset containing High-Throughput Screening (HTS) output and experimental design information. See References for details.

### Usage

    data(ex_dataMatrix)

### Format

A data frame with 80 rows and 9 columns:

- Wells. Plate well numbers for each sample

- Rows. Plate row identifiers for each sample

- Columns. Plate column identifiers for each sample

- S1_R1. Screen 1 Replicate 1

- S1_R2. Screen 1 Replicate 2

- S1_R3. Screen 1 Replicate 3

- S2_R1. Screen 2 Replicate 1

- S2_R2. Screen 2 Replicate 2

- S2_R3. Screen 2 Replicate 3

This example data matrix consists of 6 plates with 80 wells each. Although these are 96-well plates, only 80 wells in each plate contained the active compounds. Therefore, the subsequent data matrix for this package excludes the inactive wells.

### Details

The sights data format requires each plate matrix to be converted into a 1-dimensional vector. The plate wells in this vector should be arranged by row first. For example, this 3x3 plate matrix:

| Col 1 | Col 2 | Col 3
Row A | A1 | A2 | A3
Row B | B1 | B2 | B3
Row C | C1 | C2 | C3

can be converted into its vector form as:

Row | Col | Data
A | 1 | A1
A | 2 | A2
A | 3 | A3
B | 1 | B1
B | 2 | B2
B | 3 | B3
C | 1 | C1
C | 2 | C2
C | 3 | C3

Here, number of columns in a plate is 3, and number of rows is 3 as well. Each such plate vector should form a column in the data matrix before application of sights functions. Only the active wells should be included in the data matrix; inactive wells containing mock/control compounds should be marked as NAs, or if they are in entire rows/columns they can be removed completely as in this example dataset and the arguments plateRows and plateCols modified accordingly.

### Value

Dataframe of 80 rows and 9 columns as explained in Format

### References

CMBA Titration series 10uM Tyr samples. Murie et al. (2015). Improving detection of rare biological events in high-throughput screens. Journal of Biomolecular Screening, 20(2), 230-241.

### Examples

    ## load dataset
    data(ex_dataMatrix)

    ## structure of dataset
    str(ex_dataMatrix)
    ## summary of dataset
    summary(ex_dataMatrix)

    ## See help pages of SIGHTS functions for examples of using this dataset

[Package sights version 1.8.1 Index]