featureBasedData {PathwaySplice} | R Documentation

## featureBasedData

### Description

This dataset includes analysis results of RNA-seq data in Dolatshad et al. (2015), which compared transcriptome of CD34+ cells from myelodysplastic syndrome (MDS) patients with SF3B1 mutations vs. healthy controls using RNA sequencing. The `JunctionSeq` package was used to assess differential usage of counting bins, which are non-overlapping segments of the exons or splicing junctions (see Fig 1 in Anders et al. (2012)). Because of the size limit, only counting bins associated with a subset of genes were included here for demonstration.

### Usage

    data(featureBasedData)

### Format

A data frame with variables for gene identifier (`geneID`), gene feature identifier (`countbinID`), and p-value for gene feature (`pvalue`). Here we used "gene feature" and "counting bin" interchangeably

### References

H Dolatshad, A Pellagatti, M Fernandez-Mercado1, B H Yip, L Malcovati, M Attwood, B Przychodzen N Sahgal, A A Kanapin, H Lockstone, L Scifo, P Vandenberghe, E Papaemmanuil, C W J Smith, P J Campbell, S Ogawa1, J P Maciejewski, M Cazzola, K I Savage1 and J Boultwood1 (2015) Disruption of SF3B1 results in deregulated expression and splicing of key genes and pathways in myelodysplastic syndrome hematopoietic stem and progenitor cells. Leukemia (2015) 29, 1092-1103

Anders S, Reyes A, Huber W (2012) Dececting differential usage of exons from RNA-seq data. Genome Research 22(10): 2008-2017

[Package PathwaySplice version 1.4.0 Index]