autism: Autism dataset
In bapred: Batch Effect Removal and Addon Normalization (in Phenotype Prediction using Gene Data)
autism R Documentation
Autism dataset
Description
Total RNA obtained from lmyphoblast cell lines derived from 250 individuals, 137 of which suffer from autism and 113 are healthy. The dataset consists of four batches of sizes 101, 96, 45 and 8.
Usage
data(autism)
Format
1) X - the covariate matrix: a matrix of dimension 250 x 1000, containing the numerical transcript values
2) batch - the batch variable: a factor with levels '1', '2', '3' and '4'
3) y - the target variable: a factor with levels '1' corresponding to 'healthy' and '2' corresponding to 'autism'
Details
The RNA measurements were obtained by the Illumina HumanRef-8 v3.0 Expression BeadChip featuring 24,526 transcripts. To reduce computational burden of potential analyses performed using this dataset we randomly selected 1,000 of these 24,526 transcripts. Moreover, the original dataset consisted of five batches and contained measurements of 439 individuals. Again to reduce computational burden of potential analyses we excluded the biggest batch featuring 189 individuals resulting in the 250 individuals included in the dataset made available in bapred.
Source
ArrayExpress, accession number: E-GEOD-37772
References
Luo, R., Sanders, S. J., Tian, Y., Voineagu, I., Huang, N., Chu, S. H., Klei, L., Cai, C., Ou, J., Lowe, J. K., Hurles, M. E., Devlin, B., State, M. W., Geschwind, D. H. (2012). Genome-wide Transcriptome Profiling Reveals the Functional Impact of Rare De Novo and Recurrent CNVs in Autism Spectrum Disorders. The American Journal of Human Genetics 91:38–55, <doi: 10.1016/j.ajhg.2012.05.011>.
Examples
data(autism)
bapred documentation built on June 22, 2022, 9:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| autism | R Documentation |
Autism dataset
Description
Total RNA obtained from lmyphoblast cell lines derived from 250 individuals, 137 of which suffer from autism and 113 are healthy. The dataset consists of four batches of sizes 101, 96, 45 and 8.
Usage
data(autism)
Format
1) X - the covariate matrix: a matrix of dimension 250 x 1000, containing the numerical transcript values
2) batch - the batch variable: a factor with levels '1', '2', '3' and '4'
3) y - the target variable: a factor with levels '1' corresponding to 'healthy' and '2' corresponding to 'autism'
Details
The RNA measurements were obtained by the Illumina HumanRef-8 v3.0 Expression BeadChip featuring 24,526 transcripts. To reduce computational burden of potential analyses performed using this dataset we randomly selected 1,000 of these 24,526 transcripts. Moreover, the original dataset consisted of five batches and contained measurements of 439 individuals. Again to reduce computational burden of potential analyses we excluded the biggest batch featuring 189 individuals resulting in the 250 individuals included in the dataset made available in bapred.
Source
ArrayExpress, accession number: E-GEOD-37772
References
Luo, R., Sanders, S. J., Tian, Y., Voineagu, I., Huang, N., Chu, S. H., Klei, L., Cai, C., Ou, J., Lowe, J. K., Hurles, M. E., Devlin, B., State, M. W., Geschwind, D. H. (2012). Genome-wide Transcriptome Profiling Reveals the Functional Impact of Rare De Novo and Recurrent CNVs in Autism Spectrum Disorders. The American Journal of Human Genetics 91:38–55, <doi: 10.1016/j.ajhg.2012.05.011>.
Examples
data(autism)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.