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ODER()
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ODER: Optimising the Definition of Expressed Regions |
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add_expressed_genes()
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Adding the nearest expressed genes |
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annotatERs()
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Connects ERs to genes using junction data, then classifies ERs
into "exonic", "intronic", "intergenic",
or a combination of these categories |
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file_cache()
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Cache a file if it is not found locally |
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get_chr_info()
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Get information from UCSC about the chromosomes passed in |
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get_count_matrix()
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Generate the count matrix |
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get_coverage()
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Obtain the mean coverage across multiple BigWig files |
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get_ers() get_strand_ers()
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Define sets of ERs |
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get_exons() get_ers_delta() get_opt_ers()
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Obtain set of non-overlapping exons |
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gtex_SRP012682_SRX222703_lung_auc_1
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An example AUC value |
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gtex_SRP012682_SRX222703_lung_coverage_1
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An example object containing coverage |
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gtex_SRP012682_SRX222703_lung_erdelta_1
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An example set of ER deltas |
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gtex_SRP012682_SRX222703_lung_ers_1
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An example set of Expressed Regions |
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lung_junc_21_22
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Junction data of chromosomes 21 and 22 from a lung tissue sample |
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plot_ers()
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Plot Expressed regions |
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pseudogene
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Different transcript biotypes that count as pseudogene |
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refine_ERs()
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Refines the ERs start and end points |
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tissue_options
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The different tissues that can be filtered on for gene expression |