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Administrator
UPSCb-public
Commits
9504aaaa
Commit
9504aaaa
authored
Jul 07, 2015
by
Nicolas Delhomme
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Added a synthetic transcript example
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0e375a01
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Drosophila_melanogaster.BDGP5.77-synthetic-transcripts.rda
...rosophila_melanogaster.BDGP5.77-synthetic-transcripts.rda
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Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz
...syRNASeq/Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz
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synthetic-transcript-creation-example.R
tutorial/easyRNASeq/synthetic-transcript-creation-example.R
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synthetic-transcript-creation-example.html
...ial/easyRNASeq/synthetic-transcript-creation-example.html
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tutorial/easyRNASeq/Drosophila_melanogaster.BDGP5.77-synthetic-transcripts.rda
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9504aaaa
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tutorial/easyRNASeq/Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz
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9504aaaa
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tutorial/easyRNASeq/synthetic-transcript-creation-example.R
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9504aaaa
#' ---
#' title: "Synthetic transcripts generation example"
#' author: "Nicolas Delhomme"
#' date: "`r Sys.Date()`"
#' output:
#' html_document:
#' toc: true
#' number_sections: true
#' ---
#'
#' # Setup
#' Load the libraries
library
(
easyRNASeq
)
suppressPackageStartupMessages
(
library
(
IRanges
))
suppressPackageStartupMessages
(
library
(
genomeIntervals
))
library
(
pander
)
#' Source an helper file
source
(
"https://microasp.upsc.se/root/upscb-public/raw/master/src/R/createSyntheticTranscripts.R"
)
#' # Process
#' ## Synthetic transcripts creation
#' This function takes a gtf or gff3 _filename_ as input.
#'
#' The _input_ parameter defines the file format (default to gff3).
#'
#' The _feature_ parameter defines which feature to look for in the provided
#' file. Commonly mRNA for gff3 and transcript for gtf. It defaults to mRNA.
#' Several parameter can ge given as argument.
#'
#' The _output_ paramter defines the type of object that is returned.
#' It can generate a **Genome_intervals** or a __GRanges__ class of objects.
#' The former can be saved as a gff3 using the writeGff3 function from the
#' genomeIntervals package (loaded). The latter can be saved as an RData object
#' and/or be used directly in the construction of an AnnotParam.
gAnnot
<-
createSyntheticTranscripts
(
filename
=
"~/Box Sync/Projects/easyRNASeq/Drosophila_melanogaster.BDGP5.77.with-chr.gtf.gz"
,
input
=
"gtf"
,
feature
=
"transcript"
,
output
=
"GRanges"
)
#' ## Export
#' Save the object for later re-use
save
(
gAnnot
,
file
=
"Drosophila_melanogaster.BDGP5.77-synthetic-transcripts.rda"
)
#' ## Summarization
#' ### Set the params
param
<-
RnaSeqParam
(
annotParam
=
AnnotParam
(
datasource
=
gAnnot
),
bamParam
=
BamParam
(
paired
=
FALSE
))
#' ### Get the BAM files
bamFiles
<-
getBamFileList
(
filenames
=
dir
(
system.file
(
package
=
"RnaSeqTutorial"
,
"extdata"
),
pattern
=
"[A,T].*.bam$"
,
full.names
=
TRUE
))
#' ### Run
sexp
<-
simpleRNASeq
(
bamFiles
=
bamFiles
,
param
=
param
,
verbose
=
TRUE
)
#' ### Check
pander
(
colSums
(
assay
(
sexp
)))
#' # Session Info
sessionInfo
()
tutorial/easyRNASeq/synthetic-transcript-creation-example.html
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9504aaaa
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