referencePrepare: Creates reference file

In IntEREst: Intron-Exon Retention Estimator

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)

IntEREst documentation built on Nov. 8, 2020, 8:05 p.m.