ROCR: visualizing classifier performance in R

Sing, Tobias; Sander, Oliver; Beerenwinkel, Niko; Lengauer, Thomas

doi:10.1093/bioinformatics/bti623

Cited by 2,877 publications

(2,227 citation statements)

References 2 publications

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“…Third, diseases were grouped into two categories of relatively even size (see above). Models were built using the R packages caret (Kuhn, 2008) and randomForest, and ROC curves were generated with ROCR (Sing et al , 2005). …”

Section: Methodsmentioning

confidence: 99%

The landscape of human mutually exclusive splicing

Hatje

Rahman

Vidal

et al. 2017

Molecular Systems Biology

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Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA‐Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi‐cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila. Finally, MXEs are significantly enriched in pathogenic mutations and their spatio‐temporal expression might predict human disease pathology.

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Section: Methodsmentioning

confidence: 99%

The landscape of human mutually exclusive splicing

Hatje

Rahman

Vidal

et al. 2017

Molecular Systems Biology

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“…The minimal variant frequency was set to 1/10,000 (VarScan) and the poolsize was set to 10,000 (CRISP, vipR). ROC curves and the area under the ROC curve were computed for each variant frequency with the R package ROCR 32 . See Supplementary Methods for a detailed description of the chosen options.…”

Section: Methodsmentioning

confidence: 99%

Reliable detection of subclonal single-nucleotide variants in tumour cell populations

et al. 2012

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According to the clonal evolution model, tumour growth is driven by competing subclones in somatically evolving cancer cell populations, which gives rise to genetically heterogeneous tumours. Here we present a comparative targeted deep-sequencing approach combined with a customised statistical algorithm, called deepsnV, for detecting and quantifying subclonal single-nucleotide variants in mixed populations. We show in a rigorous experimental assessment that our approach is capable of detecting variants with frequencies as low as 1/10,000 alleles. In selected genomic loci of the TP53 and VHL genes isolated from matched tumour and normal samples of four renal cell carcinoma patients, we detect 24 variants at allele frequencies ranging from 0.0002 to 0.34. moreover, we demonstrate how the allele frequencies of known single-nucleotide polymorphisms can be exploited to detect loss of heterozygosity. our findings demonstrate that genomic diversity is common in renal cell carcinomas and provide quantitative evidence for the clonal evolution model.

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“…ArcGIS 10.3 was used to generate validation datasets, and Python was used for image processing (ESRI, 2014). Modelling and statistical analysis were conducted in R using the following packages: ggplot2 (Wickham, 2009), dplyr (Wickham and Francois, 2015), rasterVis (Perpinan and Hijmans, 2016), randomForest (Liaw and Wiener, 2002), reshape2 (Wickham, 2007), ROCR (Sing et al, 2005), SDMTools (VanDerWal et al, 2014), and spatial.tools (Greenberg, 2014).…”

Section: Analysis Toolsmentioning

confidence: 99%

Three decades of Landsat-derived spring surface water dynamics in an agricultural wetland mosaic; Implications for migratory shorebirds

Schaffer‐Smith

Swenson

Barbaree

et al. 2017

Remote Sensing of Environment

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Satellite measurements of surface water offer promise for understanding wetland habitat availability at broad spatial and temporal scales; reliable habitat is crucial for the persistence of migratory shorebirds that depend on wetland networks. We analyzed water extent dynamics within wetland habitats at a globally important shorebird stopover site for a 1983-2015 Landsat time series, and evaluated the effect of climate on water extent. A range of methods can detect open water from imagery, including supervised classification approaches and thresholds for spectral bands and indices. Thresholds provide a time advantage; however, there is no universally superior index, nor single best threshold for all instances. We used random forest to model the presence or absence of water from >6200 reference pixels, and derived an optimal water probability threshold for our study area using receiver operating characteristic curves. An optimized mid-infrared (1.5-1.7 μm) threshold identified open water in the Sacramento Valley of California at 30-m resolution with an average of 90% producer's accuracy, comparable to approaches that require more intensive user input. SLC-off Landsat 7 imagery was integrated by applying a customized interpolation that mapped water in missing data gaps with 99% user's accuracy. On average we detected open water on ~26000 ha (~3% of the study area) in early April at the peak of shorebird migration, while water extent increased five-fold after the migration rush. Over the last three decades, late March water extent declined by ~1300 ha per year, primarily due to changes in the extent and timing of agricultural flood-irrigation. Water within shorebird habitats was significantly associated with an index of water availability at the peak of migration. Our approach can be used to optimize thresholds for time series analysis and near-real-time mapping in other regions, and requires only marginally more time than generating a confusion matrix.

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ROCR: visualizing classifier performance in R

Abstract: tobias.sing@mpi-sb.mpg.de.

Cited by 2,877 publications

References 2 publications

The landscape of human mutually exclusive splicing

The landscape of human mutually exclusive splicing

Reliable detection of subclonal single-nucleotide variants in tumour cell populations

Three decades of Landsat-derived spring surface water dynamics in an agricultural wetland mosaic; Implications for migratory shorebirds

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