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Last data update: 2014.03.03 |
Class to contain raw Bisulfite Sequencing (BiSeq) DataDescriptionThe Objects from the ClassObjects can be created by calls of the form
However, one will most likely create a Slots
ExtendsClass Methods
Author(s)Katja Hebestreit See AlsoRangedSummarizedExperiment, Examples
showClass("BSraw")
## How to create a BSraw object by hand:
metadata <- list(Sequencer = "Sequencer", Year = "2013")
rowRanges <- GRanges(seqnames = "chr1",
ranges = IRanges(start = c(1,2,3), end = c(1,2,3)))
colData <- DataFrame(group = c("cancer", "control"),
row.names = c("sample_1", "sample_2"))
totalReads <- matrix(c(rep(10L, 3), rep(5L, 3)), ncol = 2)
methReads <- matrix(c(rep(5L, 3), rep(5L, 3)), ncol = 2)
BSraw(metadata = metadata,
rowRanges = rowRanges,
colData = colData,
totalReads = totalReads,
methReads = methReads)
## A more realistic example can be loaded:
data(rrbs)
rrbs
head(totalReads(rrbs))
head(methReads(rrbs))
Results
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> library(BiSeq)
Loading required package: S4Vectors
Loading required package: stats4
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
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Formula
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BiSeq/BSraw-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BSraw-class
> ### Title: Class to contain raw Bisulfite Sequencing (BiSeq) Data
> ### Aliases: BSraw-class BSraw BSraw,matrix,matrix,GRanges-method
> ### combine,BSraw,BSraw-method methReads methReads<- totalReads
> ### totalReads<- totalReads,BSraw-method totalReads<-,BSraw,matrix-method
> ### methReads,BSraw-method methReads<-,BSraw,matrix-method
> ### Keywords: classes
>
> ### ** Examples
>
> showClass("BSraw")
Class "BSraw" [package "BiSeq"]
Slots:
Name: rowRanges colData
Class: GenomicRangesORGRangesList DataFrame
Name: assays NAMES
Class: Assays characterORNULL
Name: elementMetadata metadata
Class: DataFrame list
Extends:
Class "RangedSummarizedExperiment", directly
Class "SummarizedExperiment", by class "RangedSummarizedExperiment", distance 2
Class "Vector", by class "RangedSummarizedExperiment", distance 3
Class "Annotated", by class "RangedSummarizedExperiment", distance 4
>
> ## How to create a BSraw object by hand:
> metadata <- list(Sequencer = "Sequencer", Year = "2013")
> rowRanges <- GRanges(seqnames = "chr1",
+ ranges = IRanges(start = c(1,2,3), end = c(1,2,3)))
> colData <- DataFrame(group = c("cancer", "control"),
+ row.names = c("sample_1", "sample_2"))
> totalReads <- matrix(c(rep(10L, 3), rep(5L, 3)), ncol = 2)
> methReads <- matrix(c(rep(5L, 3), rep(5L, 3)), ncol = 2)
> BSraw(metadata = metadata,
+ rowRanges = rowRanges,
+ colData = colData,
+ totalReads = totalReads,
+ methReads = methReads)
class: BSraw
dim: 3 2
metadata(0):
assays(2): totalReads methReads
rownames: NULL
rowData names(0):
colnames(2): sample_1 sample_2
colData names(1): group
>
> ## A more realistic example can be loaded:
> data(rrbs)
> rrbs
class: BSraw
dim: 10502 10
metadata(0):
assays(2): totalReads methReads
rownames(10502): 1456 1457 ... 4970981 4970982
rowData names(0):
colnames(10): APL1 APL2 ... APL11624 APL5894
colData names(1): group
>
> head(totalReads(rrbs))
APL1 APL2 APL3 APL7 APL8 APL10961 APL11436 APL11523 APL11624 APL5894
1456 39 6 10 0 0 48 31 65 39 29
1457 39 6 10 0 0 48 31 65 39 29
1458 39 6 10 0 0 48 27 65 39 29
1459 20 26 49 48 39 27 23 34 29 15
1460 20 26 49 48 39 27 23 34 28 15
1461 20 26 49 48 39 27 22 34 29 15
> head(methReads(rrbs))
APL1 APL2 APL3 APL7 APL8 APL10961 APL11436 APL11523 APL11624 APL5894
1456 32 6 7 0 0 15 23 16 7 7
1457 33 6 7 0 0 18 10 19 2 7
1458 33 6 10 0 0 20 10 19 2 3
1459 13 20 34 41 32 3 8 8 6 4
1460 14 18 35 37 33 2 4 4 3 0
1461 14 16 35 40 31 5 5 5 1 2
>
>
>
>
>
>
> dev.off()
null device
1
>
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