testData: Test Data: Data for function testing

In DiPALM: Differential Pattern Analysis via Linear Modeling

Test Data: Data for function testing

Description

A list of objects that can be used to test individual DiPALM functions.

Usage

data("testData")

Format

A List of 6 objects:

1. $timeCourseList - A List of 4 matrices containing mRNA expression data on Brassica rapa R500.

   • $Drought.R1 (Plants exposed to drought, Replicate 1) A matrix of time-course gene expression data [18428 Genes X 12 Time-points]

   • $Drought.R2 (Plants exposed to drought, Replicate 2) A matrix of time-course gene expression data [18428 Genes X 12 Time-points]

   • $Watered.R1 (Properly watered plants, Replicate 1) A matrix of time-course gene expression data [18428 Genes X 12 Time-points]

   • $Watered.R2 (Properly watered plants, Replicate 2) A matrix of time-course gene expression data [18428 Genes X 12 Time-points]

2. $moduleEigengenes - A dataframe [12 rows and 90 columns] representing 90 different expression vectors that describe descrete expression patterns found in the whole dataset ($timeCourseList).

   • Rows: each row represents a single time-point

   • Columns: each column represents a distinct expression pattern seen repeatedly in the full data

3. $modelDesign - A matrix [4 rows and 2 columns] used as a design matrix for a simple linear model. This matrix provides a mapping between the input instances (timeCourseList) and the two fixed effects fitted in the mode (Drought and Watered). This matrix was created with model.matrix.

4. $modelContrast - A character string specifying the contrast to be evaluated using the fitted model for each gene. This example is used to compare watered to drought conditions.

5. $testResults - A named numeric vector with 18428 values from DiPALM test results on actual data.

   • names: Gene accessions

   • values: The summed absolute values of t-values generated from limma model contrasts related to each eigengene pattern. This can be thought of as a DiPALM score for differential patterning.

6. $permutedResults- A named numeric vector with 18428 values from DiPALM test results on permuted data. This vector acts as a null distribution in order to estimate significance of actual test results.

   • names: Gene accessions

   • values: The summed absolute values of t-values generated from limma model contrasts related to each eigengene pattern using permuted expression data. This can be thought of as a null distribution of DiPALM scores for differential patterning.

Source

Data is from: Greenham et al., eLife 2017;6:e29655

DiPALM documentation built on June 28, 2022, 1:06 a.m.