targeted: Sample AlignedRead data set for targeted sequencing...

In seandavi/Rpressa: A collection of useful code for bioinformatics

Description

This is a dataset that was generated using in-solution capture technology to capture some exons of genes of interest. The regions of capture are described in another related dataset.

Usage

data(targeted)

Format

The format is: Formal class 'AlignedRead' [package "ShortRead"] with 8 slots ..@ chromosome : Factor w/ 66767 levels "0:0:1","0:0:10",..: 66767 66767 22181 7859 66767 66767 66767 66767 66767 66767 ... ..@ position : int [1:6349344] NA NA NA NA NA NA NA NA NA NA ... ..@ strand : Factor w/ 3 levels "-","+","*": NA NA NA NA NA NA NA NA NA NA ... ..@ alignQuality:Formal class 'NumericQuality' [package "ShortRead"] with 1 slots .. .. ..@ quality: int [1:6349344] 0 0 0 0 0 0 0 0 0 0 ... ..@ alignData :Formal class 'AlignedDataFrame' [package "ShortRead"] with 4 slots .. .. ..@ varMetadata :'data.frame': 7 obs. of 1 variable: .. .. .. ..$ labelDescription: chr [1:7] "Analysis pipeline run" "Flow cell lane" "Flow cell tile" "Cluster x-coordinate" ... .. .. ..@ data :'data.frame': 6349344 obs. of 7 variables: .. .. .. ..$ run : Factor w/ 1 level "90814": 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ lane : int [1:6349344] 5 5 5 5 5 5 5 5 5 5 ... .. .. .. ..$ tile : int [1:6349344] 1 1 1 1 1 1 1 1 1 1 ... .. .. .. ..$ x : int [1:6349344] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. ..$ y : int [1:6349344] 1947 1976 623 330 552 90 133 315 410 447 ... .. .. .. ..$ filtering: Factor w/ 2 levels "Y","N": 2 2 2 2 2 2 2 2 2 2 ... .. .. .. ..$ contig : Factor w/ 1 level "": 1 1 1 1 1 1 1 1 1 1 ... .. .. ..@ dimLabels : chr [1:2] "readName" "alignColumn" .. .. ..@ .__classVersion__:Formal class 'Versions' [package "Biobase"] with 1 slots .. .. .. .. ..@ .Data:List of 1 .. .. .. .. .. ..$ : int [1:3] 1 1 0 ..@ quality :Formal class 'SFastqQuality' [package "ShortRead"] with 1 slots .. .. ..@ quality:Formal class 'BStringSet' [package "Biostrings"] with 5 slots .. .. .. .. ..@ super :Formal class 'BString' [package "Biostrings"] with 6 slots .. .. .. .. .. .. ..@ xdata :Formal class 'RawPtr' [package "IRanges"] with 2 slots .. .. .. .. .. .. .. .. ..@ xp :<externalptr> .. .. .. .. .. .. .. .. ..@ .link_to_cached_object:<environment: 0x566412c> .. .. .. .. .. .. ..@ offset : int 0 .. .. .. .. .. .. ..@ length : int 253973760 .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. ..@ elementType : chr "ANYTHING" .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. .. .. ..@ start : int [1:6349344] 1 41 81 121 161 201 241 281 321 361 ... .. .. .. .. .. .. ..@ width : int [1:6349344] 40 40 40 40 40 40 40 40 40 40 ... .. .. .. .. .. .. ..@ NAMES : NULL .. .. .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. .. .. ..@ metadata : list() .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ elementType : chr "ANYTHING" .. .. .. .. ..@ metadata : list() ..@ sread :Formal class 'DNAStringSet' [package "Biostrings"] with 5 slots .. .. ..@ super :Formal class 'DNAString' [package "Biostrings"] with 6 slots .. .. .. .. ..@ xdata :Formal class 'RawPtr' [package "IRanges"] with 2 slots .. .. .. .. .. .. ..@ xp :<externalptr> .. .. .. .. .. .. ..@ .link_to_cached_object:<environment: 0x566412c> .. .. .. .. ..@ offset : int 0 .. .. .. .. ..@ length : int 253973760 .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ elementType : chr "ANYTHING" .. .. .. .. ..@ metadata : list() .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. ..@ start : int [1:6349344] 1 41 81 121 161 201 241 281 321 361 ... .. .. .. .. ..@ width : int [1:6349344] 40 40 40 40 40 40 40 40 40 40 ... .. .. .. .. ..@ NAMES : NULL .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. ..@ metadata : list() .. .. ..@ elementMetadata: NULL .. .. ..@ elementType : chr "ANYTHING" .. .. ..@ metadata : list() ..@ id :Formal class 'BStringSet' [package "Biostrings"] with 5 slots .. .. ..@ super :Formal class 'BString' [package "Biostrings"] with 6 slots .. .. .. .. ..@ xdata :Formal class 'RawPtr' [package "IRanges"] with 2 slots .. .. .. .. .. .. ..@ xp :<externalptr> .. .. .. .. .. .. ..@ .link_to_cached_object:<environment: 0x566412c> .. .. .. .. ..@ offset : int 0 .. .. .. .. ..@ length : int 0 .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ elementType : chr "ANYTHING" .. .. .. .. ..@ metadata : list() .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots .. .. .. .. ..@ start : int [1:6349344] 1 1 1 1 1 1 1 1 1 1 ... .. .. .. .. ..@ width : int [1:6349344] 0 0 0 0 0 0 0 0 0 0 ... .. .. .. .. ..@ NAMES : NULL .. .. .. .. ..@ elementMetadata: NULL .. .. .. .. ..@ elementType : chr "integer" .. .. .. .. ..@ metadata : list() .. .. ..@ elementMetadata: NULL .. .. ..@ elementType : chr "ANYTHING" .. .. ..@ metadata : list()

Source

The data were generated in the Genetics Branch, National Cancer Institute, National Institutes of Health by Ogan Abaan.

Examples

data(targeted)
targeted

seandavi/Rpressa documentation built on May 29, 2019, 4:33 p.m.