Estimated read start and insert size distributions from MiSeq data in GEO dataset GSE37704.

Description

We downloaded the fastq files, aligned with TopHat and processed with wrapKnown to obtain the estimated distributions for each of the 6 samples. distrsGSE37704 is a list with the 6 corresponding elements. The estimated distributions for HiSeq data were very similar, hence these distributions can be used as defaults for Illumina MiSeq and HiSeq experiments.

Usage

data(distrsGSE37704)

Format

An list with 6 elements of class readDistrs. See help(getDistrs) and help(readDistrs-class) for details.

Examples

data(distrsGSE37704)
distrsGSE37704
plot(distrsGSE37704[[1]],'readSt')
lines(distrsGSE37704[[2]], 'readSt', col=2)
plot(distrsGSE37704[[1]],'fragLength')

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(casper)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/casper/distrsGSE37704.Rd_%03d_medium.png", width=480, height=480)
> ### Name: distrsGSE37704
> ### Title: Estimated read start and insert size distributions from MiSeq
> ###   data in GEO dataset GSE37704.
> ### Aliases: distrsGSE37704
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(distrsGSE37704)
> distrsGSE37704
[[1]]
readDistrs object

Insert size distribution (only first few shown)
 9 10 11 12 13 14 
 1  0  0  0  0  0 
...
Read start cumulative distribution function in slot stDis

[[2]]
readDistrs object

Insert size distribution (only first few shown)
 22  23  24  25  26  27 
  2 135 147 166 187 182 
...
Read start cumulative distribution function in slot stDis

[[3]]
readDistrs object

Insert size distribution (only first few shown)
 22  23  24  25  26  27 
174 248 267 251 227 222 
...
Read start cumulative distribution function in slot stDis

[[4]]
readDistrs object

Insert size distribution (only first few shown)
 22  23  24  25  26  27 
205 262 361 310 311 326 
...
Read start cumulative distribution function in slot stDis

[[5]]
readDistrs object

Insert size distribution (only first few shown)
 22  23  24  25  26  27 
  4 121 143 155 164 172 
...
Read start cumulative distribution function in slot stDis

[[6]]
readDistrs object

Insert size distribution (only first few shown)
 22  23  24  25  26  27 
122 181 217 210 168 181 
...
Read start cumulative distribution function in slot stDis

> plot(distrsGSE37704[[1]],'readSt')
> lines(distrsGSE37704[[2]], 'readSt', col=2)
> plot(distrsGSE37704[[1]],'fragLength')
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>