| Title: | Example whole genome bisulfite data for the bsseq package |
|---|---|
| Description: | Example whole genome bisulfite data for the bsseq package |
| Authors: | Kasper Daniel Hansen |
| Maintainer: | Kasper Daniel Hansen <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 0.50.0 |
| Built: | 2026-10-10 11:05:41 UTC |
| Source: | https://github.com/bioc/bsseqData |
Whole-genome bisulfite sequencing data (WGBS) for colon cancer on chromosome 21 and 22. 3 patients were sequenced and the data contains matched colon cancer and normal colon.
data(BS.cancer.ex)data(BS.cancer.ex)
The data is stored as an object of class "BSseq".
The file ‘scripts/create_BS.cancer.R’ (see example for location) is a script that generates all data objects in this package from the raw alignment output, contained in the directory ‘umtab’ (see example for location). The raw alignment output is the output from the BSmooth alignment suite, using an old (legacy) format.
This dataset BS.cancer.ex.fit is the same basic data,
but it also contains smoothed methylation values.
Hansen, K. D. et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nature Genetics 43, 768-775.
BS.cancer.ex.fit, BS.cancer.ex.tstat
(t-statistics for this dataset) and keepLoci.ex for
related datasets and the "BSseq"
class. Also see the vignette(s) in the bsseq package.
data(BS.cancer.ex) BS.cancer.ex script <- system.file("scripts", "create_BS.cancer.R", package = "bsseqData") script readLines(script) system.file("umtab", package = "bsseqData")data(BS.cancer.ex) BS.cancer.ex script <- system.file("scripts", "create_BS.cancer.R", package = "bsseqData") script readLines(script) system.file("umtab", package = "bsseqData")
Whole-genome bisulfite sequencing data (WGBS) for colon cancer on chromosome 21 and 22. 3 patients were sequenced and the data contains matched colon cancer and normal colon. This dataset includes smoothed methylation values.
data(BS.cancer.ex.fit)data(BS.cancer.ex.fit)
The data is stored as an object of class "BSseq".
The file ‘scripts/create_BS.cancer.R’ (see example for location) is a script that generates all data objects in this package from the raw alignment output, contained in the directory ‘umtab’ (see example for location). The raw alignment output is the output from the BSmooth alignment suite, using an old (legacy) format.
This dataset is exactly like BS.cancer.ex except it also
contains smoothed methylation values.
Hansen, K. D. et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nature Genetics 43, 768-775.
BS.cancer.ex, BS.cancer.ex.tstat
(t-statistics for this dataset) and keepLoci.ex for
related datasets as well as the
"BSseq" class and the
BSmooth function. Also see the
vignette(s) in the bsseq package.
data(BS.cancer.ex.fit) BS.cancer.ex.fit script <- system.file("scripts", "create_BS.cancer.R", package = "bsseqData") script readLines(script) system.file("umtab", package = "bsseqData")data(BS.cancer.ex.fit) BS.cancer.ex.fit script <- system.file("scripts", "create_BS.cancer.R", package = "bsseqData") script readLines(script) system.file("umtab", package = "bsseqData")
T-statistics produced by the BSmooth.tstat function, run on the
BS.cancer.ex.fit object subsetted by keepLoci.ex.
data(BS.cancer.ex.tstat)data(BS.cancer.ex.tstat)
The data is stored as an object of class "BSseqTstat".
See below for the script creating this object.
Hansen, K. D. et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nature Genetics 43, 768-775.
BS.cancer.ex.fit (data used to produce the t-statistics)
and keepLoci.ex (used for subsetting) as well as the
"BSseqTstat" class and
BSmooth.tstat. Also see the
vignette(s) in the bsseq package.
data(BS.cancer.ex.tstat) BS.cancer.ex.tstat ## This script shows how the object was created script <- system.file("scripts", "create_BS.cancer.R", package = "bsseqData") script readLines(script)data(BS.cancer.ex.tstat) BS.cancer.ex.tstat ## This script shows how the object was created script <- system.file("scripts", "create_BS.cancer.R", package = "bsseqData") script readLines(script)
This object describes which methylation loci were kept, when
t-statistics were generated from BS.cancer.fit.ex using the
function BSmooth.tstat.
data(keepLoci.ex)data(keepLoci.ex)
A vector of indices into BS.cancer.fit.ex.
See below how this object was created and used.
BS.cancer.ex.fit (this is the data the subsetting index
works on) and BS.cancer.ex.tstat and the
BSmooth.tstat function . Also see
the vignette(s) in the bsseq package.
data(keepLoci.ex) ## This script shows how the object was created script <- system.file("scripts", "create_BS.cancer.R", package = "bsseqData") script readLines(script)data(keepLoci.ex) ## This script shows how the object was created script <- system.file("scripts", "create_BS.cancer.R", package = "bsseqData") script readLines(script)