referencePrepare {IntEREst} | 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 `GenomicFeatures` library for more information.
`ucscTableName` | The UCSC table name to use. See `tablename` parameter of `makeTxDbFromUCSC` function of `GenomicFeatures` library for more information.
`ucscUrl` | The UCSC URL address. See `url` parameter of `makeTxDbFromUCSC` function of `GenomicFeatures` 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 `GenomicFeatures` library for more information.
`biomartDataset` | BioMart dataset name; default is "hsapiens_gene_ensembl". See `dataset` parameter of `makeTxDbFromBiomart` function of `GenomicFeatures` 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 `GenomicFeatures` 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 `GenomicFeatures` 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 `GenomicFeatures` 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 `GenomicFeatures` 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 `GenomicFeatures` 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 `GenomicFeatures` 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)

[Package IntEREst version 1.10.2 Index]