Supported by Dr. Osamu Ogasawara and  providing  . |
|
Last data update: 2014.03.03 |
Annotation package for Illumina Infinium DNA methylation probesDescriptionThis package loads one or more FeatureDb objects. Such FeatureDb objects are an R interface to prefabricated databases contained by this package. In the case of the Infinium methylation FDb, it is FDb.InfiniumMethylation.hg18 (for the moment; hg18 may come later, or alternatively users can use liftOver() from rtracklayer to do it). Author(s)Tim Triche, Jr. See Also
Examples
## load the library
library(FDb.InfiniumMethylation.hg18)
## list the contents that are loaded into memory
ls('package:FDb.InfiniumMethylation.hg18')
## show the db object that is loaded by calling it's name
FDb.InfiniumMethylation.hg18
## extract features for use in constructing SummarizedExperiments
## or comparing chip features against other data (e.g. ChIP-seq)
InfiniumMethylation <- features(FDb.InfiniumMethylation.hg18)
## it's much more convenient to address ranges by their probe ID:
names(InfiniumMethylation) <- values(InfiniumMethylation)$name
## we'd prefer if R would stop us from comparing across assemblies:
met <- metadata(FDb.InfiniumMethylation.hg18) ## need to fetch genome
genome(InfiniumMethylation) <- met[which(met[,'name']=='Genome'),'value']
## last but not least, sort the probes in genomic order
InfiniumMethylation <- sort(InfiniumMethylation)
show(InfiniumMethylation)
## Example: probes that overlap Irizarry's HMM CpG islands
data(hg18.islands)
CGI.probes <- subsetByOverlaps(InfiniumMethylation, hg18.islands)
head(CGI.probes)
tail(CGI.probes)
## Same as above, but now for "shores"
hg18.shores <- c(flank(hg18.islands, 2000, start=TRUE),
flank(hg18.islands, 2000, start=FALSE))
shore.probes <- subsetByOverlaps(InfiniumMethylation, hg18.shores)
head(shore.probes)
tail(shore.probes)
## The same logic works for overlapping probes with other data.
## For example, we can easily do this for old 27k data as well:
hm27 <- get27k()
hm27.shores <- subsetByOverlaps(hm27, hg18.shores)
## The same approach works to overlap (e.g.) ChIP-seq peaks or DNAseI footprints
## Much more data is available via GenomicFeatures and rtracklayer:
help(makeFeatureDbFromUCSC)
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.
You are welcome to redistribute it under certain conditions.
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(FDb.InfiniumMethylation.hg18)
Loading required package: GenomicFeatures
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: GenomicRanges
Loading required package: AnnotationDbi
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: TxDb.Hsapiens.UCSC.hg18.knownGene
Loading required package: org.Hs.eg.db
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/FDb.InfiniumMethylation.hg18/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FDb.InfiniumMethylation.hg18
> ### Title: Annotation package for Illumina Infinium DNA methylation probes
> ### Aliases: FDb.InfiniumMethylation.hg18-package
> ### FDb.InfiniumMethylation.hg18
> ### Keywords: package data
>
> ### ** Examples
>
>
> ## load the library
> library(FDb.InfiniumMethylation.hg18)
>
> ## list the contents that are loaded into memory
> ls('package:FDb.InfiniumMethylation.hg18')
[1] "FDb.InfiniumMethylation.hg18" "get27k"
[3] "get450k" "getNearest"
[5] "getNearestGene" "getNearestTSS"
[7] "getNearestTranscript" "getPlatform"
>
> ## show the db object that is loaded by calling it's name
> FDb.InfiniumMethylation.hg18
FeatureDb object:
| Db type: FeatureDb
| Supporting package: GenomicFeatures
| data_nrow: 487117
| Db created by: GenomicFeatures package from Bioconductor
| Creation time: 2012-08-16 13:51:50 -0700 (Thu, 16 Aug 2012)
| GenomicFeatures version at creation time: 1.9.28
| RSQLite version at creation time: 0.11.1
| DBSCHEMAVERSION: 1.0
| Data source: NCBI/GEO and dbSNP
| Genome: hg18
| Resource: Illumina Infinium DNA methylation probes, aligned to hg18
| Genus and Species: Homo sapiens
| URL: ftp://ftp.illumina.com
Please see: help('select') for usage information
>
> ## extract features for use in constructing SummarizedExperiments
> ## or comparing chip features against other data (e.g. ChIP-seq)
> InfiniumMethylation <- features(FDb.InfiniumMethylation.hg18)
>
> ## it's much more convenient to address ranges by their probe ID:
> names(InfiniumMethylation) <- values(InfiniumMethylation)$name
>
> ## we'd prefer if R would stop us from comparing across assemblies:
> met <- metadata(FDb.InfiniumMethylation.hg18) ## need to fetch genome
> genome(InfiniumMethylation) <- met[which(met[,'name']=='Genome'),'value']
>
> ## last but not least, sort the probes in genomic order
> InfiniumMethylation <- sort(InfiniumMethylation)
> show(InfiniumMethylation)
GRanges object with 487117 ranges and 14 metadata columns:
seqnames ranges strand | addressA_450 addressB_450
<Rle> <IRanges> <Rle> | <character> <character>
[1] chr16 [ 438, 439] * | 24771476
[2] chr16 [ 748, 749] * | 36644319 45624454
[3] chr16 [ 1085, 1086] * | 65765435
[4] chr16 [ 2460, 2461] * | 28717484
[5] chr16 [13243, 13244] * | 42725455
... ... ... ... . ... ...
[487113] chrY [25418818, 25418819] * | 73757458
[487114] chrY [25619722, 25619723] * | 61745505
[487115] chrY [26964924, 26964925] * | 56793430
[487116] chrY [26964938, 26964939] * | 67794346 26610401
[487117] chrY [26965300, 26965301] * | 16749405
addressA_27 addressB_27 channel450 channel27 probeType
<character> <character> <character> <character> <character>
[1] <NA> <NA> Both <NA> cg
[2] <NA> <NA> Red <NA> cg
[3] <NA> <NA> Both <NA> cg
[4] <NA> <NA> Both <NA> cg
[5] <NA> <NA> Both <NA> cg
... ... ... ... ... ...
[487113] <NA> <NA> Both <NA> cg
[487114] <NA> <NA> Both <NA> cg
[487115] <NA> <NA> Both <NA> cg
[487116] <NA> <NA> Red <NA> cg
[487117] <NA> <NA> Both <NA> cg
percentGC platform
<character> <character>
[1] 0.58 HM450
[2] 0.76 HM450
[3] 0.56 HM450
[4] 0.66 HM450
[5] 0.64 HM450
... ... ...
[487113] 0.42 HM450
[487114] 0.44 HM450
[487115] 0.66 HM450
[487116] 0.68 HM450
[487117] 0.48 HM450
sourceSeq probeStart
<character> <character>
[1] TTTCGGTGGTACTGCGAAGGCAGAGCAGAGTTCTGCTCAGGTCAGACCCG 438
[2] CGCCCCCAGGCCGGCGCCGTGCGACTTTGCTCCTGCAACACACGCCCCCC 700
[3] CAGCTAGGGACATTGCAGGCTCCTCTTGCTCAAAGTGTAGTGGCAGCACG 1037
[4] CGGCCCAGTAGAGCCCTAGGGGTGACGCCACTCCCACTCACTGTCGACTC 2412
[5] ATGGAGGCTTGGGCGGGTCACCCCCAGTGCAGGCCAAGATGCAGGTTACG 13195
... ... ...
[487113] CGCCTAAATAAGAATAGGAGTAAAGGAGAGTATTACCTCCAAATCACCGG 25418818
[487114] CGTCACCTGGATGCTGGTTTAAGTGATATATGAAAATCCACCCTAAGGAC 25619722
[487115] CGGATCTTTCTGACCAGCCCCGGCCCCATCTTGGCCTTACCTGGCCTCCC 26964876
[487116] CGGCTCCCAACGCTCGGATCTTTCTGACCAGCCCCGGCCCCATCTTGGCC 26964890
[487117] TGGTATTGGTGAAGTCTACCACTCCAGCTCGTAGACTTCCATAATCGTCG 26965300
probeEnd probeTarget probeExtension
<character> <character> <character>
[1] 487 438 <NA>
[2] 749 748 749.0
[3] 1086 1085 1086.0
[4] 2461 2460 2461.0
[5] 13244 13243 13244.0
... ... ... ...
[487113] 25418867 25418818 <NA>
[487114] 25619771 25619722 <NA>
[487115] 26964925 26964924 26964925.0
[487116] 26964939 26964938 26964939.0
[487117] 26965349 26965300 <NA>
-------
seqinfo: 24 sequences from hg18 genome; no seqlengths
>
> ## Example: probes that overlap Irizarry's HMM CpG islands
> data(hg18.islands)
> CGI.probes <- subsetByOverlaps(InfiniumMethylation, hg18.islands)
> head(CGI.probes)
GRanges object with 6 ranges and 14 metadata columns:
seqnames ranges strand | addressA_450 addressB_450 addressA_27
<Rle> <IRanges> <Rle> | <character> <character> <character>
[1] chr16 [ 438, 439] * | 24771476 <NA>
[2] chr16 [ 748, 749] * | 36644319 45624454 <NA>
[3] chr16 [13243, 13244] * | 42725455 <NA>
[4] chr16 [43423, 43424] * | 43674431 39692304 <NA>
[5] chr16 [43531, 43532] * | 22723389 27762328 <NA>
[6] chr16 [43568, 43569] * | 71649315 12766458 <NA>
addressB_27 channel450 channel27 probeType percentGC platform
<character> <character> <character> <character> <character> <character>
[1] <NA> Both <NA> cg 0.58 HM450
[2] <NA> Red <NA> cg 0.76 HM450
[3] <NA> Both <NA> cg 0.64 HM450
[4] <NA> Grn <NA> cg 0.72 HM450
[5] <NA> Red <NA> cg 0.62 HM450
[6] <NA> Red <NA> cg 0.66 HM450
sourceSeq probeStart
<character> <character>
[1] TTTCGGTGGTACTGCGAAGGCAGAGCAGAGTTCTGCTCAGGTCAGACCCG 438
[2] CGCCCCCAGGCCGGCGCCGTGCGACTTTGCTCCTGCAACACACGCCCCCC 700
[3] ATGGAGGCTTGGGCGGGTCACCCCCAGTGCAGGCCAAGATGCAGGTTACG 13195
[4] ACAGAGGCAGACGCCGGGGCTGGCGGCGATGGAGCAGCAGTCGGAGGACG 43375
[5] CGCTGCCACCGCTTCTCCTGCAACACGTGCCCCTACGTGCACAACATCAC 43483
[6] CGGGGCAGAACAGCAGCATGGTCTCGAACTCCGCAGGCTCCAACTCCCGG 43568
probeEnd probeTarget probeExtension
<character> <character> <character>
[1] 487 438 <NA>
[2] 749 748 749.0
[3] 13244 13243 13244.0
[4] 43424 43423 43424.0
[5] 43532 43531 43532.0
[6] 43617 43568 <NA>
-------
seqinfo: 24 sequences from hg18 genome; no seqlengths
> tail(CGI.probes)
GRanges object with 6 ranges and 14 metadata columns:
seqnames ranges strand | addressA_450 addressB_450
<Rle> <IRanges> <Rle> | <character> <character>
[1] chrY [22863046, 22863047] * | 47649309
[2] chrY [22863145, 22863146] * | 27741501 71708483
[3] chrY [22864315, 22864316] * | 74720388
[4] chrY [22959063, 22959064] * | 24631411 26605360
[5] chrY [22959113, 22959114] * | 53806306
[6] chrY [26965300, 26965301] * | 16749405
addressA_27 addressB_27 channel450 channel27 probeType percentGC
<character> <character> <character> <character> <character> <character>
[1] <NA> <NA> Both <NA> cg 0.64
[2] <NA> <NA> Red <NA> cg 0.7
[3] <NA> <NA> Both <NA> cg 0.66
[4] <NA> <NA> Red <NA> cg 0.56
[5] <NA> <NA> Both <NA> cg 0.56
[6] <NA> <NA> Both <NA> cg 0.48
platform sourceSeq
<character> <character>
[1] HM450 CGGCGCCCACCCACTGCTGCCAGCCATCCCGAATTGACAGCTGCAAGGAT
[2] HM450 CGGTAAATGCCCCAGGCCGCGGGACATCCCCGGCTTCTGGGCCAGAGCCA
[3] HM450 GCGGAGGGGCCTCAGGACTCGCCCACAGCCTTTGCAGTAACTGGCTGACG
[4] HM450 CGTACGCCTGAGGGCCAGGCGAACCTCAGGCTCTTTGTCCTACTAAAAAG
[5] HM450 TACGCCTGAGGGCCAGGCGAACCTCAGGCTCTTTGTCCTACTAAAAAGCG
[6] HM450 TGGTATTGGTGAAGTCTACCACTCCAGCTCGTAGACTTCCATAATCGTCG
probeStart probeEnd probeTarget probeExtension
<character> <character> <character> <character>
[1] 22863046 22863095 22863046 <NA>
[2] 22863097 22863146 22863145 22863146.0
[3] 22864267 22864316 22864315 22864316.0
[4] 22959063 22959112 22959063 <NA>
[5] 22959065 22959114 22959113 22959114.0
[6] 26965300 26965349 26965300 <NA>
-------
seqinfo: 24 sequences from hg18 genome; no seqlengths
>
> ## Same as above, but now for "shores"
> hg18.shores <- c(flank(hg18.islands, 2000, start=TRUE),
+ flank(hg18.islands, 2000, start=FALSE))
> shore.probes <- subsetByOverlaps(InfiniumMethylation, hg18.shores)
> head(shore.probes)
GRanges object with 6 ranges and 14 metadata columns:
seqnames ranges strand | addressA_450 addressB_450 addressA_27
<Rle> <IRanges> <Rle> | <character> <character> <character>
[1] chr16 [ 1085, 1086] * | 65765435 <NA>
[2] chr16 [ 2460, 2461] * | 28717484 <NA>
[3] chr16 [13243, 13244] * | 42725455 <NA>
[4] chr16 [41260, 41261] * | 38765355 <NA>
[5] chr16 [41686, 41687] * | 47645328 1740168
[6] chr16 [42121, 42122] * | 36735483 5550563
addressB_27 channel450 channel27 probeType percentGC platform
<character> <character> <character> <character> <character> <character>
[1] <NA> Both <NA> cg 0.56 HM450
[2] <NA> Both <NA> cg 0.66 HM450
[3] <NA> Both <NA> cg 0.64 HM450
[4] <NA> Both <NA> cg 0.4 HM450
[5] 840379 Both Grn cg 0.36 BOTH
[6] 510215 Both Red cg 0.44 BOTH
sourceSeq probeStart
<character> <character>
[1] CAGCTAGGGACATTGCAGGCTCCTCTTGCTCAAAGTGTAGTGGCAGCACG 1037
[2] CGGCCCAGTAGAGCCCTAGGGGTGACGCCACTCCCACTCACTGTCGACTC 2412
[3] ATGGAGGCTTGGGCGGGTCACCCCCAGTGCAGGCCAAGATGCAGGTTACG 13195
[4] TTGAGTGCCTCTTATATACCAAGCACGGTATAATTCACTTTATGCTCTCG 41212
[5] TTTGTTACCTAACAAAAACAACACTTCAGACTCCAAGTAACTGAATAGCG 41638
[6] CGTCAGTCTTAATGTTTGCATGCTACTCCAGTTTGTACTGTGTTGTGGGA 42073
probeEnd probeTarget probeExtension
<character> <character> <character>
[1] 1086 1085 1086.0
[2] 2461 2460 2461.0
[3] 13244 13243 13244.0
[4] 41261 41260 41261.0
[5] 41687 41686 41687.0
[6] 42122 42121 42122.0
-------
seqinfo: 24 sequences from hg18 genome; no seqlengths
> tail(shore.probes)
GRanges object with 6 ranges and 14 metadata columns:
seqnames ranges strand | addressA_450 addressB_450
<Rle> <IRanges> <Rle> | <character> <character>
[1] chrY [22863145, 22863146] * | 27741501 71708483
[2] chrY [22863915, 22863916] * | 53713392 <NA>
[3] chrY [22864315, 22864316] * | 74720388
[4] chrY [26964924, 26964925] * | 56793430
[5] chrY [26964938, 26964939] * | 67794346 26610401
[6] chrY [26965300, 26965301] * | 16749405
addressA_27 addressB_27 channel450 channel27 probeType percentGC
<character> <character> <character> <character> <character> <character>
[1] <NA> <NA> Red <NA> cg 0.7
[2] <NA> <NA> Both <NA> cg 0.5
[3] <NA> <NA> Both <NA> cg 0.66
[4] <NA> <NA> Both <NA> cg 0.66
[5] <NA> <NA> Red <NA> cg 0.68
[6] <NA> <NA> Both <NA> cg 0.48
platform sourceSeq
<character> <character>
[1] HM450 CGGTAAATGCCCCAGGCCGCGGGACATCCCCGGCTTCTGGGCCAGAGCCA
[2] HM450 CGTTGCTGGGGTGGAATTTGTCTGCAATAGAAGCTGAAACCCCACAAGGA
[3] HM450 GCGGAGGGGCCTCAGGACTCGCCCACAGCCTTTGCAGTAACTGGCTGACG
[4] HM450 CGGATCTTTCTGACCAGCCCCGGCCCCATCTTGGCCTTACCTGGCCTCCC
[5] HM450 CGGCTCCCAACGCTCGGATCTTTCTGACCAGCCCCGGCCCCATCTTGGCC
[6] HM450 TGGTATTGGTGAAGTCTACCACTCCAGCTCGTAGACTTCCATAATCGTCG
probeStart probeEnd probeTarget probeExtension
<character> <character> <character> <character>
[1] 22863097 22863146 22863145 22863146.0
[2] 22863867 22863916 22863915 22863916.0
[3] 22864267 22864316 22864315 22864316.0
[4] 26964876 26964925 26964924 26964925.0
[5] 26964890 26964939 26964938 26964939.0
[6] 26965300 26965349 26965300 <NA>
-------
seqinfo: 24 sequences from hg18 genome; no seqlengths
>
> ## The same logic works for overlapping probes with other data.
> ## For example, we can easily do this for old 27k data as well:
> hm27 <- get27k()
Fetching coordinates for hg18...
> hm27.shores <- subsetByOverlaps(hm27, hg18.shores)
>
> ## The same approach works to overlap (e.g.) ChIP-seq peaks or DNAseI footprints
> ## Much more data is available via GenomicFeatures and rtracklayer:
> help(makeFeatureDbFromUCSC)
makeFeatureDbFromUCSC package:GenomicFeatures R Documentation
_M_a_k_i_n_g _a _F_e_a_t_u_r_e_D_b _o_b_j_e_c_t _f_r_o_m _a_n_n_o_t_a_t_i_o_n_s _a_v_a_i_l_a_b_l_e _a_t _t_h_e _U_C_S_C _G_e_n_o_m_e
_B_r_o_w_s_e_r
_D_e_s_c_r_i_p_t_i_o_n:
The 'makeFeatureDbFromUCSC' function allows the user to make a
FeatureDb object from simple annotation tracks at UCSC. The
tracks in question must (at a minimum) have a start, end and a
chromosome affiliation in order to be made into a FeatureDb. This
function requires a precise declaration of its first three
arguments to indicate which genome, track and table wish to be
imported. There are discovery functions provided to make this
process go smoothly.
_U_s_a_g_e:
supportedUCSCFeatureDbTracks(genome)
supportedUCSCFeatureDbTables(genome, track)
UCSCFeatureDbTableSchema(genome,
track,
tablename)
makeFeatureDbFromUCSC(
genome,
track,
tablename,
columns = UCSCFeatureDbTableSchema(genome,track,tablename),
url="http://genome.ucsc.edu/cgi-bin/",
goldenPath_url="http://hgdownload.cse.ucsc.edu/goldenPath",
chromCol,
chromStartCol,
chromEndCol,
taxonomyId=NA)
_A_r_g_u_m_e_n_t_s:
genome: genome abbreviation used by UCSC and obtained by
'ucscGenomes()[ , "db"]'. For example: '"hg18"'.
track: name of the UCSC track. Use 'supportedUCSCFeatureDbTracks'
to get the list of available tracks for a particular genome
tablename: name of the UCSC table containing the annotations to
retrieve. Use the 'supportedUCSCFeatureDbTables' utility
function to get the list of supported tables for a track.
columns: a named character vector to list out the names and types of
the other columns that the downloaded track should have. Use
'UCSCFeatureDbTableSchema' to retrieve this information for a
particular table.
url,goldenPath_url: use to specify the location of an alternate UCSC
Genome Browser.
chromCol: If the schema comes back and the 'chrom' column has been
labeled something other than 'chrom', use this argument to
indicate what that column has been labeled as so we can
properly designate it. This could happen (for example) with
the knownGene track tables, which has no 'chromStart' or
'chromEnd' columns, but which DOES have columns that could
reasonably substitute for these columns under particular
circumstances. Therefore we allow these three columns to
have arguments so that their definition can be re-specified
chromStartCol: Same thing as chromCol, but for renames of 'chromStart'
chromEndCol: Same thing as chromCol, but for renames of 'chromEnd'
taxonomyId: By default this value is NA and the organism inferred will
be used to look up the correct value for this. But you can
use this argument to override that and supply your own valid
taxId here.
_D_e_t_a_i_l_s:
'makeFeatureDbFromUCSC' is a convenience function that builds a
tiny database from one of the UCSC track tables.
'supportedUCSCFeatureDbTracks' a convenience function that returns
potential track names that could be used to make FeatureDb objects
'supportedUCSCFeatureDbTables' a convenience function that returns
potential table names for FeatureDb objects (table names go with a
track name) 'UCSCFeatureDbTableSchema' A convenience function that
creates a named vector of types for all the fields that can
potentially be supported for a given track. By default, this will
be called on your specified tablename to include all of the fields
in a track.
_V_a_l_u_e:
A FeatureDb object for 'makeFeatureDbFromUCSC'. Or in the case of
'supportedUCSCFeatureDbTracks' and 'UCSCFeatureDbTableSchema' a
named character vector
_A_u_t_h_o_r(_s):
M. Carlson
_S_e_e _A_l_s_o:
'ucscGenomes',
_E_x_a_m_p_l_e_s:
## Display the list of genomes available at UCSC:
library(GenomicFeatures)
library(rtracklayer)
ucscGenomes()[ , "db"]
## Display the list of Tracks supported by makeFeatureDbFromUCSC():
# supportedUCSCFeatureDbTracks("mm10")
## Display the list of tables supported by your track:
supportedUCSCFeatureDbTables(genome="mm10",
track="qPCR Primers")
## Display fields that could be passed in to colnames:
UCSCFeatureDbTableSchema(genome="mm10",
track="qPCR Primers",
tablename="qPcrPrimers")
## Retrieving a full transcript dataset for Mouse from UCSC:
fdb <- makeFeatureDbFromUCSC(genome="mm10",
track="qPCR Primers",
tablename="qPcrPrimers")
fdb
>
>
>
>
>
>
> dev.off()
null device
1
>
|
Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and