recount.rpkm.RData

This is the output of a pipeline that trains a Pathway-Level Information ExtractoR (PLIER) model on recount2 data (RPKM). See: https://github.com/greenelab/rheum-plier-data/tree/978c37938383ff7adcadacfcbc35931ce5e62b17

It was run in a Docker container. See the Github repository for more information.

Below, we include information about the scripts used to generate each item using the relative path from the repo top directory.

It contains:
* The rse-gene files downloaded from the recount bioconductor package (recount_experiments_rse-gene.tar.gz, output of recount2/1-get_all_recount_dataset.R)
* The RPKM normalized recount data (recount_rpkm.RDS, output of recount2/2-prep_recount_for_plier.R)
* The recount data processed for use with PLIER, the pathway data prepped for use with PLIER, and the k parameter for use with PLIER (recount_data_prep_PLIER.RDS, output of recount2/2-prep_recount_for_plier.R)
* The PLIER model itself (recount_PLIER_model.RDS, output of recount2/3-run_recount_plier.R)

If you use any of this data, please be sure to cite:

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B and Leek JT (2017). "Reproducible RNA-seq analysis using recount2." Nature Biotechnology. doi: 10.1038/nbt.3838

And the PLIER preprint, if you use the PLIER model:

Mao W, Harmann B, Sealfon SC, Zaslavsky E, and Chikina M (2017). "Pathway-Level Information ExtractoR (PLIER) for gene expression data." bioRxiv. doi: 10.1101/116061

本数据集为某分析流水线的输出产物，该流水线基于recount2数据集的RPKM数据训练通路水平信息提取器（Pathway-Level Information ExtractoR, PLIER）模型。相关细节可参见：https://github.com/greenelab/rheum-plier-data/tree/978c37938383ff7adcadacfcbc35931ce5e62b17。

本数据集通过Docker容器运行生成，更多信息可查阅对应GitHub仓库。

下文将基于仓库根目录的相对路径，说明用于生成各数据项的脚本信息：
* 从recount Bioconductor包中下载的rse-gene文件：recount_experiments_rse-gene.tar.gz，为recount2/1-get_all_recount_dataset.R的输出结果；
* 经RPKM标准化处理的recount数据集：recount_rpkm.RDS，为recount2/2-prep_recount_for_plier.R的输出结果；
* 适配PLIER的预处理recount数据集、适配PLIER的通路数据集，以及PLIER所需的k参数文件：recount_data_prep_PLIER.RDS，为recount2/2-prep_recount_for_plier.R的输出结果；
* PLIER模型本身的保存文件：recount_PLIER_model.RDS，为recount2/3-run_recount_plier.R的输出结果。

若使用本数据集，请务必引用以下文献：
Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B 与 Leek JT (2017). 《使用recount2开展可重复的RNA测序分析》，《自然·生物技术》. DOI: 10.1038/nbt.3838

若使用PLIER模型，请同时引用该模型的预印本文献：
Mao W, Harmann B, Sealfon SC, Zaslavsky E, 与 Chikina M (2017). 《用于基因表达数据的通路水平信息提取器（PLIER）》，bioRxiv. DOI: 10.1101/116061