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Last data update: 2014.03.03 |
Generate GTF files for transcript visualization in genome browsersDescriptionGenerate GTF files for transcript visualization in genome browsers. UsagegenerateGTF(transcriptData, filters=NULL, expressionCutoff=0,scoreMethod="local", filePrefix="spliceR_transcripts", shortDescription="SpliceR Transcripts", longDescription="Transcripts generated by SpliceR", useProgressBar=T) Arguments
Details
Author(s)Kristoffer Vitting-Seerup, Johannes Waage ReferencesVitting-Seerup K, Porse BT, Sandelin A, Waage JE. (2013) spliceR: An R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. PeerJ PrePrints 1:e80v1 Examples
#Load cufflinks example data
cuffDB <- prepareCuffExample()
#Generate SpliceRList from cufflinks data
cuffDB_spliceR <- prepareCuff(cuffDB)
#Reduce dataset size for fast example runtime
cuffDB_spliceR[[1]] <- cuffDB_spliceR[[1]][1:500]
#Run spliceR
mySpliceRList <- spliceR(cuffDB_spliceR, compareTo='preTranscript', filters=c('expressedGenes','geneOK', 'isoOK', 'expressedIso', 'isoClass'))
#Export to GTF
generateGTF(mySpliceRList, filters=c("geneOK", "isoOK", "expressedGenes", "expressedIso"), scoreMethod="local")
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)
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> library(spliceR)
Loading required package: cummeRbund
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: RSQLite
Loading required package: DBI
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: fastcluster
Attaching package: 'fastcluster'
The following object is masked from 'package:stats':
hclust
Loading required package: rtracklayer
Loading required package: GenomicRanges
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: Gviz
Loading required package: grid
Attaching package: 'cummeRbund'
The following object is masked from 'package:GenomicRanges':
promoters
The following object is masked from 'package:IRanges':
promoters
The following object is masked from 'package:BiocGenerics':
conditions
Loading required package: VennDiagram
Loading required package: futile.logger
Loading required package: RColorBrewer
Loading required package: plyr
Attaching package: 'plyr'
The following object is masked from 'package:cummeRbund':
count
The following object is masked from 'package:IRanges':
desc
The following object is masked from 'package:S4Vectors':
rename
Attaching package: 'spliceR'
The following object is masked from 'package:cummeRbund':
conditions
The following object is masked from 'package:BiocGenerics':
conditions
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/spliceR/generateGTF.Rd_%03d_medium.png", width=480, height=480)
> ### Name: generateGTF
> ### Title: Generate GTF files for transcript visualization in genome
> ### browsers
> ### Aliases: generateGTF
>
> ### ** Examples
>
> #Load cufflinks example data
> cuffDB <- prepareCuffExample()
Creating database /tmp/RtmpKnDwAT/cuffData.db
Reading Run Info File /tmp/RtmpKnDwAT/run.info
Writing runInfo Table
Reading Read Group Info /tmp/RtmpKnDwAT/read_groups.info
Writing replicates Table
Reading GTF file
Writing GTF features to 'features' table...
Reading /tmp/RtmpKnDwAT/genes.fpkm_tracking
Checking samples table...
Populating samples table...
Writing genes table
Reshaping geneData table
Recasting
Writing geneData table
Reading /tmp/RtmpKnDwAT/gene_exp.diff
Writing geneExpDiffData table
Reading /tmp/RtmpKnDwAT/promoters.diff
Writing promoterDiffData table
Reading /tmp/RtmpKnDwAT/genes.count_tracking
Reshaping geneCount table
Recasting
Writing geneCount table
Reading read group info in /tmp/RtmpKnDwAT/genes.read_group_tracking
Writing geneReplicateData table
Reading /tmp/RtmpKnDwAT/isoforms.fpkm_tracking
Checking samples table...
OK!
Writing isoforms table
Reshaping isoformData table
Recasting
Writing isoformData table
Reading /tmp/RtmpKnDwAT/isoform_exp.diff
Writing isoformExpDiffData table
Reading /tmp/RtmpKnDwAT/isoforms.count_tracking
Reshaping isoformCount table
Recasting
Writing isoformCount table
Reading read group info in /tmp/RtmpKnDwAT/isoforms.read_group_tracking
Writing isoformReplicateData table
Reading /tmp/RtmpKnDwAT/tss_groups.fpkm_tracking
Checking samples table...
OK!
Writing TSS table
Reshaping TSSData table
Recasting
Writing TSSData table
Reading /tmp/RtmpKnDwAT/tss_group_exp.diff
Writing TSSExpDiffData table
Reading /tmp/RtmpKnDwAT/splicing.diff
Writing splicingDiffData table
Reading /tmp/RtmpKnDwAT/tss_groups.count_tracking
Reshaping TSSCount table
Recasting
Writing TSSCount table
Reading read group info in /tmp/RtmpKnDwAT/tss_groups.read_group_tracking
Writing TSSReplicateData table
Reading /tmp/RtmpKnDwAT/cds.fpkm_tracking
Checking samples table...
OK!
Writing CDS table
Reshaping CDSData table
Recasting
Writing CDSData table
Reading /tmp/RtmpKnDwAT/cds_exp.diff
Writing CDSExpDiffData table
Reading /tmp/RtmpKnDwAT/cds.diff
Writing CDSDiffData table
Reading /tmp/RtmpKnDwAT/cds.count_tracking
Reshaping CDSCount table
Recasting
Writing CDSCount table
Reading read group info in /tmp/RtmpKnDwAT/cds.read_group_tracking
Writing CDSReplicateData table
Indexing Tables...
Warning messages:
1: attributes are not identical across measure variables; they will be dropped
2: attributes are not identical across measure variables; they will be dropped
3: attributes are not identical across measure variables; they will be dropped
4: attributes are not identical across measure variables; they will be dropped
5: attributes are not identical across measure variables; they will be dropped
6: attributes are not identical across measure variables; they will be dropped
7: attributes are not identical across measure variables; they will be dropped
8: attributes are not identical across measure variables; they will be dropped
>
> #Generate SpliceRList from cufflinks data
> cuffDB_spliceR <- prepareCuff(cuffDB)
Reading cuffDB, isoforms...
Reading cuffDB, exons...
Analyzing cufflinks annotation problem...
Fixing cufflinks annotation problem...
Cufflinks annotation problem was fixed for 65 Cuff_genes
Creating spliceRList...
>
> #Reduce dataset size for fast example runtime
> cuffDB_spliceR[[1]] <- cuffDB_spliceR[[1]][1:500]
>
> #Run spliceR
> mySpliceRList <- spliceR(cuffDB_spliceR, compareTo='preTranscript', filters=c('expressedGenes','geneOK', 'isoOK', 'expressedIso', 'isoClass'))
Preparing transcript data...
Converting to internal objects...
167 isoforms pre-filtering...
Filtering...
78 isoforms post-filtering...
Preparing exons...
Analyzing transcripts...
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Preparing output...
Done in 1.5 secs
>
> #Export to GTF
> generateGTF(mySpliceRList, filters=c("geneOK", "isoOK", "expressedGenes", "expressedIso"), scoreMethod="local")
Preparing transcript data...
167 isoforms pre-filtering...
Converting to internal objects...
Filtering...
105 isoforms post-filtering...
Generating GTFs...
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Writing GTFs...
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> dev.off()
null device
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