referencePrepare: Creates reference file
In gacatag/IntEREst: Intron-Exon Retention Estimator
View source: R/referencePrepare.R
referencePrepare R Documentation
Creates reference file
Description
Creates reference file for IntEREst functions, e.g. interest(). The
function uses functions of biomaRt library.
Usage
referencePrepare( outFileTranscriptsAnnotation="",
annotateGeneIds=TRUE,
u12IntronsChr=c(), u12IntronsBeg=c(), u12IntronsEnd=c(),
u12IntronsRef, collapseExons=TRUE, sourceBuild="UCSC",
ucscGenome="hg19", ucscTableName="knownGene",
ucscUrl="http://genome-euro.ucsc.edu/cgi-bin/",
biomart="ENSEMBL_MART_ENSEMBL",
biomartDataset="hsapiens_gene_ensembl",
biomartTranscriptIds=NULL, biomartExtraFilters=NULL,
biomartIdPrefix="ensembl_", biomartHost="www.ensembl.org",
biomartPort=80, circSeqs="", miRBaseBuild=NA, taxonomyId=NA,
filePath="", fileFormat=c("auto", "gff3", "gtf"), fileDatSrc=NA,
fileOrganism=NA, fileChrInf=NULL,
fileDbXrefTag=c(), addCollapsedTranscripts=TRUE,
ignore.strand=FALSE )
Arguments
outFileTranscriptsAnnotation
If defined outputs transcripts annotations.
annotateGeneIds
Wether annotate and add the gene ids information.
collapseExons
Whether collapse (i.e. reduce) the exonic regions. TRUE by default.
sourceBuild
The source to use to build the reference data, "UCSC", "biomaRt",
and "file" (for GFF3 or GTF files) are supported.
ucscGenome
The genome to use. "hg19" is the default. See genome parameter of
makeTxDbFromUCSC function of
txdbmaker library for more information.
ucscTableName
The UCSC table name to use. See tablename parameter of
makeTxDbFromUCSC function of
txdbmaker library for more information.
ucscUrl
The UCSC URL address. See url parameter of
makeTxDbFromUCSC function of
txdbmaker library for more information.
u12IntronsChr
A vector of character strings that includes chromsomal locations of the U12
type introns. If defined together with u12IntronsBeg and
u12IntronsBeg, they would be used to annotate the U12-type introns.
u12IntronsBeg
A vector of numbers that defines the begin (or start) coordinates of the
u12-type introns.
u12IntronsEnd
A vector of numbers that defines the end coordinates of the u12-type introns.
u12IntronsRef
A GRanges object that includes the coordinates of the U12 type introns. If
defined, it would be used to annotate the U12-type introns.
biomart
BioMart database name. See biomart parameter of
makeTxDbFromBiomart function of
txdbmaker library for more information.
biomartDataset
BioMart dataset name; default is "hsapiens_gene_ensembl". See dataset
parameter of makeTxDbFromBiomart function of
txdbmaker library for more information.
biomartTranscriptIds
optional parameter to only retrieve transcript annotation results for a defined
set of transcript ids. See transcript_ids parameter of
makeTxDbFromBiomart function of
txdbmaker library for more information.
biomartExtraFilters
A list of names; i.e. additional filters to use in the BioMart query. See
filters parameter of makeTxDbFromBiomart
function of txdbmaker library for more information.
biomartIdPrefix
A list of names; i.e. additional filters to use in the BioMart query. See
id_prefix parameter of
makeTxDbFromBiomart function of
txdbmaker library for more information.
biomartHost
Host to connect to; the default is "www.ensembl.org". For older versions of the
GRCH you can provide the archive websites, e.g. for GRCH37 you can use
"grch37.ensembl.org".
biomartPort
The port to use in the HTTP communication with the host. Default is 80.
circSeqs
A character vector that includes chromosomes that should be marked as circular.
See circ_seqs parameter of
makeTxDbFromBiomart and
makeTxDbFromUCSC functions of
txdbmaker library for more information.
miRBaseBuild
Set appropriate build Information from mirbase.db to use for microRNAs
(default=NA). See miRBaseBuild parameter of
makeTxDbFromBiomart and
makeTxDbFromUCSC functions of
txdbmaker library for more information.
taxonomyId
This parameter can be used to provide taxonomy Ids. It is set to NA by default.
You can check the taxonomy Ids with the available.species() function in
GenomeInfoDb package. For more information see taxonomyId
parameter of makeTxDbFromBiomart and
makeTxDbFromUCSC functions of
txdbmaker library.
filePath
Character string i.e. the path to file. Used if sourceBuild is
"file".
fileFormat
The format of the input file. "auto", "gff3" and "gtf" is
supported.
fileDatSrc
Character string describing the source of the data file. Used if
sourceBuild is "file".
fileOrganism
The genus and species name of the organism. Used if sourceBuild is
"file".
fileChrInf
Dataframe that includes information about the chromosome. The first column
represents the chromosome name and the second column is the length of the
chromosome. Used if sourceBuild is "file".
fileDbXrefTag
A vector of chracater strings which if defined it would be used as feature
names. Used if sourceBuild is "file".
addCollapsedTranscripts
Whether add a column that includes the collapsed transcripts information. Used
if collapseExons is TRUE.
ignore.strand
Whether consider the strands in the reference. If set TURE the strands
would be ingnored.
Value
Data frame that includes the coordinates and annotations of the introns and
exons of the transcripts, i.e. the reference.
Author(s)
Ali Oghabian
Examples
# Build test gff3 data
tmpGen<- u12[u12[,"ens_trans_id"]=="ENST00000413811",]
tmpEx<-tmpGen[tmpGen[,"int_ex"]=="exon",]
exonDat<- cbind(tmpEx[,3], ".",
tmpEx[,c(7,4,5)], ".", tmpEx[,6], ".",paste("ID=exon",
tmpEx[,11], "; Parent=ENST00000413811", sep="") )
trDat<- c(tmpEx[1,3], ".", "mRNA", as.numeric(min(tmpEx[,4])),
as.numeric(max(tmpEx[,5])), ".", tmpEx[1,6], ".",
"ID=ENST00000413811")
outDir<- file.path(tempdir(),"tmpFolder")
dir.create(outDir)
outDir<- normalizePath(outDir)
gff3File=paste(outDir, "gffFile.gff", sep="/")
cat("##gff-version 3\n",file=gff3File, append=FALSE)
cat(paste(paste(trDat, collapse="\t"),"\n", sep=""),
file=gff3File, append=TRUE)
write.table(exonDat, gff3File,
row.names=FALSE, col.names=FALSE,
sep='\t', quote=FALSE, append=TRUE)
# Selecting U12 introns info from 'u12' data
u12Int<-u12[u12$int_ex=="intron"&u12$int_type=="U12",]
# Test the function
refseqRef<- referencePrepare (sourceBuild="file",
filePath=gff3File, u12IntronsChr=u12Int[,"chr"],
u12IntronsBeg=u12Int[,"begin"],
u12IntronsEnd=u12Int[,"end"], collapseExons=TRUE,
fileFormat="gff3", annotateGeneIds=FALSE)
gacatag/IntEREst documentation built on July 29, 2024, 1:12 a.m.
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View source: R/referencePrepare.R
| referencePrepare | R Documentation |
Creates reference file
Description
Creates reference file for IntEREst functions, e.g. interest(). The
function uses functions of biomaRt library.
Usage
referencePrepare( outFileTranscriptsAnnotation="",
annotateGeneIds=TRUE,
u12IntronsChr=c(), u12IntronsBeg=c(), u12IntronsEnd=c(),
u12IntronsRef, collapseExons=TRUE, sourceBuild="UCSC",
ucscGenome="hg19", ucscTableName="knownGene",
ucscUrl="http://genome-euro.ucsc.edu/cgi-bin/",
biomart="ENSEMBL_MART_ENSEMBL",
biomartDataset="hsapiens_gene_ensembl",
biomartTranscriptIds=NULL, biomartExtraFilters=NULL,
biomartIdPrefix="ensembl_", biomartHost="www.ensembl.org",
biomartPort=80, circSeqs="", miRBaseBuild=NA, taxonomyId=NA,
filePath="", fileFormat=c("auto", "gff3", "gtf"), fileDatSrc=NA,
fileOrganism=NA, fileChrInf=NULL,
fileDbXrefTag=c(), addCollapsedTranscripts=TRUE,
ignore.strand=FALSE )
Arguments
outFileTranscriptsAnnotation |
If defined outputs transcripts annotations. |
annotateGeneIds |
Wether annotate and add the gene ids information. |
collapseExons |
Whether collapse (i.e. reduce) the exonic regions. TRUE by default. |
sourceBuild |
The source to use to build the reference data, |
ucscGenome |
The genome to use. |
ucscTableName |
The UCSC table name to use. See |
ucscUrl |
The UCSC URL address. See |
u12IntronsChr |
A vector of character strings that includes chromsomal locations of the U12
type introns. If defined together with |
u12IntronsBeg |
A vector of numbers that defines the begin (or start) coordinates of the u12-type introns. |
u12IntronsEnd |
A vector of numbers that defines the end coordinates of the u12-type introns. |
u12IntronsRef |
A GRanges object that includes the coordinates of the U12 type introns. If defined, it would be used to annotate the U12-type introns. |
biomart |
BioMart database name. See |
biomartDataset |
BioMart dataset name; default is "hsapiens_gene_ensembl". See |
biomartTranscriptIds |
optional parameter to only retrieve transcript annotation results for a defined
set of transcript ids. See |
biomartExtraFilters |
A list of names; i.e. additional filters to use in the BioMart query. See
|
biomartIdPrefix |
A list of names; i.e. additional filters to use in the BioMart query. See
|
biomartHost |
Host to connect to; the default is "www.ensembl.org". For older versions of the GRCH you can provide the archive websites, e.g. for GRCH37 you can use "grch37.ensembl.org". |
biomartPort |
The port to use in the HTTP communication with the host. Default is 80. |
circSeqs |
A character vector that includes chromosomes that should be marked as circular.
See |
miRBaseBuild |
Set appropriate build Information from mirbase.db to use for microRNAs
(default=NA). See |
taxonomyId |
This parameter can be used to provide taxonomy Ids. It is set to NA by default.
You can check the taxonomy Ids with the |
filePath |
Character string i.e. the path to file. Used if |
fileFormat |
The format of the input file. |
fileDatSrc |
Character string describing the source of the data file. Used if
|
fileOrganism |
The genus and species name of the organism. Used if |
fileChrInf |
Dataframe that includes information about the chromosome. The first column
represents the chromosome name and the second column is the length of the
chromosome. Used if |
fileDbXrefTag |
A vector of chracater strings which if defined it would be used as feature
names. Used if |
addCollapsedTranscripts |
Whether add a column that includes the collapsed transcripts information. Used
if |
ignore.strand |
Whether consider the strands in the reference. If set |
Value
Data frame that includes the coordinates and annotations of the introns and exons of the transcripts, i.e. the reference.
Author(s)
Ali Oghabian
Examples
# Build test gff3 data
tmpGen<- u12[u12[,"ens_trans_id"]=="ENST00000413811",]
tmpEx<-tmpGen[tmpGen[,"int_ex"]=="exon",]
exonDat<- cbind(tmpEx[,3], ".",
tmpEx[,c(7,4,5)], ".", tmpEx[,6], ".",paste("ID=exon",
tmpEx[,11], "; Parent=ENST00000413811", sep="") )
trDat<- c(tmpEx[1,3], ".", "mRNA", as.numeric(min(tmpEx[,4])),
as.numeric(max(tmpEx[,5])), ".", tmpEx[1,6], ".",
"ID=ENST00000413811")
outDir<- file.path(tempdir(),"tmpFolder")
dir.create(outDir)
outDir<- normalizePath(outDir)
gff3File=paste(outDir, "gffFile.gff", sep="/")
cat("##gff-version 3\n",file=gff3File, append=FALSE)
cat(paste(paste(trDat, collapse="\t"),"\n", sep=""),
file=gff3File, append=TRUE)
write.table(exonDat, gff3File,
row.names=FALSE, col.names=FALSE,
sep='\t', quote=FALSE, append=TRUE)
# Selecting U12 introns info from 'u12' data
u12Int<-u12[u12$int_ex=="intron"&u12$int_type=="U12",]
# Test the function
refseqRef<- referencePrepare (sourceBuild="file",
filePath=gff3File, u12IntronsChr=u12Int[,"chr"],
u12IntronsBeg=u12Int[,"begin"],
u12IntronsEnd=u12Int[,"end"], collapseExons=TRUE,
fileFormat="gff3", annotateGeneIds=FALSE)
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