NA19240 – 3 million reads from chromosome 6 derived from 1000 genomes bam file

Description

NA19240 – 3 million reads from chromosome 6 derived from 1000 genomes bam file

Usage

data(n240)

Format

The format is:
List of 1
$ :List of 13
..$ qname : chr [1:3000000] "EAS254_13:7:88:1639:15041" "EAS139_43:2:31:1128:9551" "EAS254_13:8:68:520:6861" "BGI-FC20AHFAAXX_6_26_477:352" ...
..$ flag : int [1:3000000] 35 35 35 16 35 35 35 0 35 35 ...
..$ rname : Factor w/ 1 level "6": 1 1 1 1 1 1 1 1 1 1 ...
..$ strand: Factor w/ 3 levels "-","+","*": 2 2 2 1 2 2 2 2 2 2 ...
..$ pos : int [1:3000000] 5001 5002 5004 5004 5005 5010 5012 5018 5018 5023 ...
..$ qwidth: int [1:3000000] 51 51 51 36 51 51 36 36 36 45 ...
..$ mapq : int [1:3000000] 0 0 0 0 0 0 0 0 0 0 ...
..$ cigar : chr [1:3000000] "51M" "51M" "51M" "36M" ...
..$ mrnm : Factor w/ 1 level "6": 1 1 1 NA 1 1 1 NA 1 1 ...
..$ mpos : int [1:3000000] 5163 5203 5170 NA 5156 5183 5199 NA 5252 5273 ...
..$ isize : int [1:3000000] 214 253 218 NA 203 225 224 NA 271 296 ...
..$ seq :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: 0xc5354b8>
.. .. .. .. ..@ offset : int 0
.. .. .. .. ..@ length : int 118321039
.. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. ..@ elementType : chr "ANYTHING"
.. .. .. .. ..@ metadata : list()
.. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. ..@ start : int [1:3000000] 1 52 103 154 190 241 292 328 364 400 ...
.. .. .. .. ..@ width : int [1:3000000] 51 51 51 36 51 51 36 36 36 45 ...
.. .. .. .. ..@ NAMES : NULL
.. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. ..@ metadata : list()
.. .. ..@ elementMetadata: NULL
.. .. ..@ elementType : chr "ANYTHING"
.. .. ..@ metadata : list()
..$ qual :Formal class 'PhredQuality' [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: 0xc5354b8>
.. .. .. .. ..@ offset : int 0
.. .. .. .. ..@ length : int 118321039
.. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. ..@ elementType : chr "ANYTHING"
.. .. .. .. ..@ metadata : list()
.. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. ..@ start : int [1:3000000] 1 52 103 154 190 241 292 328 364 400 ...
.. .. .. .. ..@ width : int [1:3000000] 51 51 51 36 51 51 36 36 36 45 ...
.. .. .. .. ..@ NAMES : NULL
.. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. ..@ metadata : list()
.. .. ..@ elementMetadata: NULL
.. .. ..@ elementType : chr "ANYTHING"
.. .. ..@ metadata : list()

Details

result of Rsamtools scanBam applied to a 3mm line excerpt from the SLX chr6 aligned reads for NA19240

update october 2010 to reflect modifications to cigar handling in Rsamtools

Source

1000 genomes pilot data

Examples

data(n240)
sapply(n240[[1]], class)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ind1KG)
Loading required package: chopsticks
Loading required package: survival
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ind1KG/n240.Rd_%03d_medium.png", width=480, height=480)
> ### Name: n240
> ### Title: NA19240 - 3 million reads from chromosome 6 derived from 1000
> ###   genomes bam file
> ### Aliases: n240
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(n240)
> sapply(n240[[1]], class)
         qname           flag          rname         strand            pos 
   "character"      "integer"       "factor"       "factor"      "integer" 
        qwidth           mapq          cigar           mrnm           mpos 
     "integer"      "integer"    "character"       "factor"      "integer" 
         isize            seq           qual 
     "integer" "DNAStringSet" "PhredQuality" 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>