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Last data update: 2014.03.03 |
Getters for TargetExperiment object.DescriptionObtain TargetExperiment's slot information, according to the given function call. UsagegetBedFile(object) ## S4 method for signature 'TargetExperiment' getBedFile(object) getBamFile(object) ## S4 method for signature 'TargetExperiment' getBamFile(object) getFastaFile(object) ## S4 method for signature 'TargetExperiment' getFastaFile(object) getFeaturePanel(object) ## S4 method for signature 'TargetExperiment' getFeaturePanel(object) getGenePanel(object) ## S4 method for signature 'TargetExperiment' getGenePanel(object) getFeature(object) ## S4 method for signature 'TargetExperiment' getFeature(object) getAttribute(object) ## S4 method for signature 'TargetExperiment' getAttribute(object) getScanBamP(object) ## S4 method for signature 'TargetExperiment' getScanBamP(object) getPileupP(object) ## S4 method for signature 'TargetExperiment' getPileupP(object) getRegion(object, level, ID, collapse = TRUE) ## S4 method for signature 'TargetExperiment' getRegion(object, level, ID, collapse = TRUE) getLowCtsFeatures(object, level, threshold = 50) ## S4 method for signature 'TargetExperiment' getLowCtsFeatures(object, level, threshold = 50) Arguments
Valueaccording to the call one of the following objects can be returned
Notesee full example in Author(s)Gabriela A. Merino gmerino@bdmg.com.ar Cristobal Fresno cfresno@bdmg.com.ar and Elmer A. Fernandez efernandez@bdmg.com.ar See Also
Examples## Loading the TargetExperiment object data(ampliPanel,package="TarSeqQC") ## Get the bedFile slot getBedFile(ampliPanel) ## Get the bamFile slot getBamFile(ampliPanel) ## Get the fastaFile slot getFastaFile(ampliPanel) ## Get the feateurePanel slot getFeaturePanel(ampliPanel) ## Get the genePanel slot getGenePanel(ampliPanel) ## Get the Feature slot getFeature(ampliPanel) ## Get the attribute slot getAttribute(ampliPanel) ## Get the scanBamP slot getScanBamP(ampliPanel) ## Get the pileupP slot getPileupP(ampliPanel) ## Get the region related to a feature or a gene getRegion(ampliPanel, level="gene", ID="gene7", collapse=FALSE) ## Get the low counts features getLowCtsFeatures(ampliPanel, level="feature") Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(TarSeqQC)
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: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Loading required package: ggplot2
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:XVector':
compact
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Loading required package: openxlsx
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/TarSeqQC/TargetExperiment-getters.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getBedFile
> ### Title: Getters for TargetExperiment object.
> ### Aliases: getAttribute getAttribute,TargetExperiment-method
> ### getAttribute-methods getBamFile getBamFile,TargetExperiment-method
> ### getBamFile-methods getBedFile getBedFile,TargetExperiment-method
> ### getBedFile-methods getFastaFile getFastaFile,TargetExperiment-method
> ### getFastaFile-methods getFeature getFeature,TargetExperiment-method
> ### getFeature-methods getFeaturePanel
> ### getFeaturePanel,TargetExperiment-method getFeaturePanel-methods
> ### getGenePanel getGenePanel,TargetExperiment-method
> ### getGenePanel-methods getLowCtsFeatures
> ### getLowCtsFeatures,TargetExperiment-method getLowCtsFeatures-methods
> ### getPileupP getPileupP,TargetExperiment-method getPileupP-methods
> ### getRegion getRegion,TargetExperiment-method getRegion-methods
> ### getScanBamP getScanBamP,TargetExperiment-method getScanBamP-methods
>
> ### ** Examples
>
> ## Loading the TargetExperiment object
> data(ampliPanel,package="TarSeqQC")
> ## Get the bedFile slot
> getBedFile(ampliPanel)
GRanges object with 29 ranges and 1 metadata column:
seqnames ranges strand | gene
<Rle> <IRanges> <Rle> | <character>
AMPL1 chr1 [ 463, 551] * | gene1
AMPL2 chr1 [1553, 1603] * | gene2
AMPL3 chr1 [3766, 3814] * | gene2
AMPL4 chr3 [ 1, 59] * | gene3
AMPL5 chr3 [1062, 1125] * | gene4
... ... ... ... . ...
AMPL25 chr10 [ 97170, 97220] * | gene8
AMPL26 chr10 [102869, 102927] * | gene8
AMPL27 chr10 [102982, 103061] * | gene8
AMPL28 chr10 [105983, 106035] * | gene8
AMPL29 chr10 [106083, 106172] * | gene8
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
> ## Get the bamFile slot
> getBamFile(ampliPanel)
class: BamFile
path: ./mybam.bam
index: ./mybam.bam.bai
isOpen: FALSE
yieldSize: NA
obeyQname: FALSE
asMates: FALSE
qnamePrefixEnd: NA
qnameSuffixStart: NA
> ## Get the fastaFile slot
> getFastaFile(ampliPanel)
class: FaFile
path: ./myfasta.fa
index: ./myfasta.fa.fai
isOpen: FALSE
yieldSize: NA
> ## Get the feateurePanel slot
> getFeaturePanel(ampliPanel)
GRanges object with 29 ranges and 6 metadata columns:
seqnames ranges strand | gene gc coverage
<Rle> <IRanges> <Rle> | <character> <numeric> <numeric>
AMPL1 chr1 [ 463, 551] * | gene1 0.674 320
AMPL2 chr1 [1553, 1603] * | gene2 0.451 550
AMPL3 chr1 [3766, 3814] * | gene2 0.531 455
AMPL4 chr3 [ 1, 59] * | gene3 0.492 0
AMPL5 chr3 [1062, 1125] * | gene4 0.359 222
... ... ... ... . ... ... ...
AMPL25 chr10 [ 97170, 97220] * | gene8 0.392 126
AMPL26 chr10 [102869, 102927] * | gene8 0.424 310
AMPL27 chr10 [102982, 103061] * | gene8 0.425 556
AMPL28 chr10 [105983, 106035] * | gene8 0.358 318
AMPL29 chr10 [106083, 106172] * | gene8 0.278 184
sdCoverage medianCounts IQRCounts
<numeric> <numeric> <numeric>
AMPL1 19 326 24
AMPL2 90 574 14
AMPL3 12 463 27
AMPL4 0 0 0
AMPL5 44 247 48
... ... ... ...
AMPL25 13 130 12
AMPL26 50 314 35
AMPL27 96 601 76
AMPL28 35 335 26
AMPL29 16 190 11
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
> ## Get the genePanel slot
> getGenePanel(ampliPanel)
GRanges object with 8 ranges and 4 metadata columns:
seqnames ranges strand | medianCounts IQRCounts coverage
<Rle> <IRanges> <Rle> | <numeric> <numeric> <numeric>
gene1 chr1 [ 463, 551] * | 326 0 320
gene2 chr1 [ 1553, 3814] * | 518 56 502
gene3 chr3 [ 1, 59] * | 0 0 0
gene4 chr3 [ 1062, 23124] * | 247 419 383
gene5 chr7 [ 51, 38098] * | 251 141 262
gene6 chr7 [49567, 77951] * | 442 212 434
gene7 chr10 [ 141, 8527] * | 408 331 337
gene8 chr10 [ 9529, 106172] * | 197 164 257
sdCoverage
<numeric>
gene1 0
gene2 67
gene3 0
gene4 358
gene5 138
gene6 289
gene7 204
gene8 154
-------
seqinfo: 4 sequences from an unspecified genome; no seqlengths
> ## Get the Feature slot
> getFeature(ampliPanel)
[1] "amplicon"
> ## Get the attribute slot
> getAttribute(ampliPanel)
[1] "coverage"
> ## Get the scanBamP slot
> getScanBamP(ampliPanel)
class: ScanBamParam
bamFlag (NA unless specified):
bamSimpleCigar: FALSE
bamReverseComplement: FALSE
bamTag:
bamTagFilter:
bamWhich: 29 ranges
bamWhat:
bamMapqFilter: NA
> ## Get the pileupP slot
> getPileupP(ampliPanel)
class: PileupParam
max_depth: 1000; min_base_quality: 13; min_mapq: 0;
min_nucleotide_depth: 1; min_minor_allele_depth: 0;
distinguish_strands: TRUE; distinguish_nucleotides: TRUE;
ignore_query_Ns: TRUE; include_deletions: TRUE; include_insertions:
FALSE; left_bins: numeric(0); query_bins: numeric(0)
> ## Get the region related to a feature or a gene
> getRegion(ampliPanel, level="gene", ID="gene7", collapse=FALSE)
names seqname start end gene
1 AMPL18 chr10 141 233 gene7
2 AMPL19 chr10 1007 1079 gene7
3 AMPL20 chr10 4866 4928 gene7
4 AMPL21 chr10 6632 6693 gene7
5 AMPL22 chr10 8475 8527 gene7
> ## Get the low counts features
> getLowCtsFeatures(ampliPanel, level="feature")
names seqname start end gene gc coverage sdCoverage medianCounts
1 AMPL4 chr3 1 59 gene3 0.492 0 0 0
IQRCounts
1 0
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> dev.off()
null device
1
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