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Last data update: 2014.03.03 |
Make a RangedSummarizedExperiment object from an ExpressionSet and vice-versaDescriptionCoercion between RangedSummarizedExperiment and ExpressionSet is supported in both directions. For going from ExpressionSet to
RangedSummarizedExperiment, the
Usage
makeSummarizedExperimentFromExpressionSet(from,
mapFun=naiveRangeMapper,
...)
## range mapping functions
naiveRangeMapper(from)
probeRangeMapper(from)
geneRangeMapper(txDbPackage, key = "ENTREZID")
Arguments
Value
The range mapping functions return a GRanges object, with the
Author(s)Jim Hester, james.f.hester@gmail.com See Also
Examples
## ---------------------------------------------------------------------
## GOING FROM ExpressionSet TO RangedSummarizedExperiment
## ---------------------------------------------------------------------
data(sample.ExpressionSet, package="Biobase")
# 2 equivalent ways of doing the naive coercion
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)
as(sample.ExpressionSet, "RangedSummarizedExperiment")
# using probe range mapper
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)
# using the gene range mapper
makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet,
geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))
## ---------------------------------------------------------------------
## GOING FROM RangedSummarizedExperiment TO ExpressionSet
## ---------------------------------------------------------------------
example(RangedSummarizedExperiment) # to create 'rse'
rse
as(rse, "ExpressionSet")
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(SummarizedExperiment)
Loading required package: GenomicRanges
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
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: IRanges
Loading required package: GenomeInfoDb
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")'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SummarizedExperiment/makeSummarizedExperimentFromExpressionSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: makeSummarizedExperimentFromExpressionSet
> ### Title: Make a RangedSummarizedExperiment object from an ExpressionSet
> ### and vice-versa
> ### Aliases: makeSummarizedExperimentFromExpressionSet naiveRangeMapper
> ### probeRangeMapper geneRangeMapper
> ### coerce,ExpressionSet,RangedSummarizedExperiment-method
> ### coerce,RangedSummarizedExperiment,ExpressionSet-method
> ### coerce,SummarizedExperiment,ExpressionSet-method
> ### Keywords: manip
>
> ### ** Examples
>
> ## ---------------------------------------------------------------------
> ## GOING FROM ExpressionSet TO RangedSummarizedExperiment
> ## ---------------------------------------------------------------------
>
> data(sample.ExpressionSet, package="Biobase")
>
> # 2 equivalent ways of doing the naive coercion
> makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet)
class: RangedSummarizedExperiment
dim: 500 26
metadata(3): experimentData annotation protocolData
assays(2): exprs se.exprs
rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(3): sex type score
> as(sample.ExpressionSet, "RangedSummarizedExperiment")
class: RangedSummarizedExperiment
dim: 500 26
metadata(3): experimentData annotation protocolData
assays(2): exprs se.exprs
rownames(500): AFFX-MurIL2_at AFFX-MurIL10_at ... 31738_at 31739_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(3): sex type score
>
> # using probe range mapper
> makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet, probeRangeMapper)
'select()' returned 1:many mapping between keys and columns
class: RangedSummarizedExperiment
dim: 354 26
metadata(3): experimentData annotation protocolData
assays(2): exprs se.exprs
rownames(354): AFFX-HUMISGF3A/M97935_5_at AFFX-HUMISGF3A/M97935_MA_at
... 31736_at 31737_at
rowData names(0):
colnames(26): A B ... Y Z
colData names(3): sex type score
Warning messages:
1: In .deprecatedColsMessage() :
Accessing gene location information via 'CHR','CHRLOC','CHRLOCEND' is
deprecated. Please use a range based accessor like genes(), or select()
with columns values like TXCHROM and TXSTART on a TxDb or OrganismDb
object instead.
2: 146 probes could not be mapped.
>
> # using the gene range mapper
> makeSummarizedExperimentFromExpressionSet(sample.ExpressionSet,
+ geneRangeMapper("TxDb.Hsapiens.UCSC.hg19.knownGene"))
'select()' returned 1:many mapping between keys and columns
class: RangedSummarizedExperiment
dim: 331 26
metadata(3): experimentData annotation protocolData
assays(2): exprs se.exprs
rownames(331): AFFX-HUMISGF3A/M97935_5_at AFFX-HUMISGF3A/M97935_5_at
... 31736_at 31737_at
rowData names(1): gene_id
colnames(26): A B ... Y Z
colData names(3): sex type score
Warning message:
169 probes could not be mapped.
>
> ## ---------------------------------------------------------------------
> ## GOING FROM RangedSummarizedExperiment TO ExpressionSet
> ## ---------------------------------------------------------------------
>
> example(RangedSummarizedExperiment) # to create 'rse'
RngdSE> nrows <- 200; ncols <- 6
RngdSE> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
RngdSE> rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
RngdSE+ IRanges(floor(runif(200, 1e5, 1e6)), width=100),
RngdSE+ strand=sample(c("+", "-"), 200, TRUE),
RngdSE+ feature_id=sprintf("ID%03d", 1:200))
RngdSE> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
RngdSE+ row.names=LETTERS[1:6])
RngdSE> rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
RngdSE+ rowRanges=rowRanges, colData=colData)
RngdSE> rse
class: RangedSummarizedExperiment
dim: 200 6
metadata(0):
assays(1): counts
rownames: NULL
rowData names(1): feature_id
colnames(6): A B ... E F
colData names(1): Treatment
RngdSE> dim(rse)
[1] 200 6
RngdSE> dimnames(rse)
[[1]]
NULL
[[2]]
[1] "A" "B" "C" "D" "E" "F"
RngdSE> assayNames(rse)
[1] "counts"
RngdSE> head(assay(rse))
A B C D E F
[1,] 9499.761 7031.571 2591.5844 6886.931 8220.292 9631.723
[2,] 2656.991 7371.272 1181.8730 5802.887 6487.127 2664.323
[3,] 6146.817 1909.953 525.4137 5677.161 7359.891 7766.353
[4,] 2121.819 3235.342 984.1765 5254.603 1548.752 7893.282
[5,] 6599.005 8669.629 3060.1926 4653.174 4853.539 3418.082
[6,] 8099.391 3158.599 913.8810 4225.905 7331.335 3044.385
RngdSE> assays(rse) <- endoapply(assays(rse), asinh)
RngdSE> head(assay(rse))
A B C D E F
[1,] 9.852169 9.551313 8.553172 9.530528 9.707508 9.865965
[2,] 8.578097 9.598493 7.768003 9.359258 9.470722 8.580852
[3,] 9.416837 8.247981 6.957334 9.337354 9.596948 9.650703
[4,] 8.353176 8.775037 7.584953 9.260007 8.038352 9.666914
[5,] 9.487821 9.760728 8.719380 9.138452 9.180611 8.829982
[6,] 9.692691 8.751031 7.510848 9.042136 9.593060 8.714201
RngdSE> rowRanges(rse)
GRanges object with 200 ranges and 1 metadata column:
seqnames ranges strand | feature_id
<Rle> <IRanges> <Rle> | <character>
[1] chr1 [597744, 597843] + | ID001
[2] chr1 [412119, 412218] - | ID002
[3] chr1 [461106, 461205] + | ID003
[4] chr1 [497343, 497442] + | ID004
[5] chr1 [707754, 707853] + | ID005
... ... ... ... . ...
[196] chr2 [521527, 521626] - | ID196
[197] chr2 [438383, 438482] + | ID197
[198] chr2 [404815, 404914] + | ID198
[199] chr2 [862832, 862931] + | ID199
[200] chr2 [625920, 626019] + | ID200
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengths
RngdSE> rowData(rse) # same as 'mcols(rowRanges(rse))'
DataFrame with 200 rows and 1 column
feature_id
<character>
1 ID001
2 ID002
3 ID003
4 ID004
5 ID005
... ...
196 ID196
197 ID197
198 ID198
199 ID199
200 ID200
RngdSE> colData(rse)
DataFrame with 6 rows and 1 column
Treatment
<character>
A ChIP
B Input
C ChIP
D Input
E ChIP
F Input
RngdSE> rse[, rse$Treatment == "ChIP"]
class: RangedSummarizedExperiment
dim: 200 3
metadata(0):
assays(1): counts
rownames: NULL
rowData names(1): feature_id
colnames(3): A C E
colData names(1): Treatment
RngdSE> ## cbind() combines objects with the same ranges but different samples:
RngdSE> rse1 <- rse
RngdSE> rse2 <- rse1[,1:3]
RngdSE> colnames(rse2) <- letters[1:ncol(rse2)]
RngdSE> cmb1 <- cbind(rse1, rse2)
RngdSE> dim(cmb1)
[1] 200 9
RngdSE> dimnames(cmb1)
[[1]]
NULL
[[2]]
[1] "A" "B" "C" "D" "E" "F" "a" "b" "c"
RngdSE> ## rbind() combines objects with the same samples but different ranges:
RngdSE> rse1 <- rse
RngdSE> rse2 <- rse1[1:50,]
RngdSE> rownames(rse2) <- letters[1:nrow(rse2)]
RngdSE> cmb2 <- rbind(rse1, rse2)
RngdSE> dim(cmb2)
[1] 250 6
RngdSE> dimnames(cmb2)
[[1]]
[1] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[19] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[37] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[55] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[73] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[91] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[109] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[127] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[145] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[163] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[181] "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" "" ""
[199] "" "" "a" "b" "c" "d" "e" "f" "g" "h" "i" "j" "k" "l" "m" "n" "o" "p"
[217] "q" "r" "s" "t" "u" "v" "w" "x" "y" "z" NA NA NA NA NA NA NA NA
[235] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[[2]]
[1] "A" "B" "C" "D" "E" "F"
RngdSE> ## Coercion to/from SummarizedExperiment:
RngdSE> se0 <- as(rse, "SummarizedExperiment")
RngdSE> se0
class: SummarizedExperiment
dim: 200 6
metadata(0):
assays(1): counts
rownames: NULL
rowData names(1): feature_id
colnames(6): A B ... E F
colData names(1): Treatment
RngdSE> as(se0, "RangedSummarizedExperiment")
class: RangedSummarizedExperiment
dim: 200 6
metadata(0):
assays(1): counts
rownames: NULL
rowData names(0):
colnames(6): A B ... E F
colData names(1): Treatment
RngdSE> ## Setting rowRanges on a SummarizedExperiment object turns it into a
RngdSE> ## RangedSummarizedExperiment object:
RngdSE> se <- se0
RngdSE> rowRanges(se) <- rowRanges
RngdSE> se # RangedSummarizedExperiment
class: RangedSummarizedExperiment
dim: 200 6
metadata(0):
assays(1): counts
rownames: NULL
rowData names(1): feature_id
colnames(6): A B ... E F
colData names(1): Treatment
RngdSE> ## Sanity checks:
RngdSE> stopifnot(identical(assays(se0), assays(rse)))
RngdSE> stopifnot(identical(dim(se0), dim(rse)))
RngdSE> stopifnot(identical(dimnames(se0), dimnames(rse)))
RngdSE> stopifnot(identical(rowData(se0), rowData(rse)))
RngdSE> stopifnot(identical(colData(se0), colData(rse)))
> rse
class: RangedSummarizedExperiment
dim: 200 6
metadata(0):
assays(1): counts
rownames: NULL
rowData names(1): feature_id
colnames(6): A B ... E F
colData names(1): Treatment
> as(rse, "ExpressionSet")
ExpressionSet (storageMode: environment)
assayData: 200 features, 6 samples
element names: exprs
protocolData: none
phenoData
sampleNames: A B ... F (6 total)
varLabels: Treatment
varMetadata: labelDescription
featureData
featureNames: 1 2 ... 200 (200 total)
fvarLabels: seqnames start ... feature_id (6 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:
Warning message:
In asMethod(object) :
No assay named 'exprs' found, renaming counts to 'exprs'.
>
>
>
>
>
> dev.off()
null device
1
>
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Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and