interest.sequential: Wrapup function: Sequential running

In gacatag/IntEREst: Intron-Exon Retention Estimator

Wrapup function: Sequential running

Description

A read summarization function that countsns all the reads mapping to the introns/exons based on the users detailed parameter settings. The process runs on a single computing core.

Usage

interest.sequential( bamFileYieldSize=1000000, bamFile, isPaired,
	isPairedDuplicate=FALSE, isSingleReadDuplicate=NA, 
	reference, referenceGeneNames, 
	referenceIntronExon, repeatsTableToFilter=c(), 
	junctionReadsOnly=FALSE, outFile, logFile="", 
	returnObj= FALSE, method=c("ExEx", "IntRet", "IntSpan", "ExSkip"), 
	strandSpecific, appendLogFile=FALSE, sampleName="",
	scaleLength= c(TRUE,FALSE), scaleFragment= c(TRUE,TRUE), 
	limitRanges=GRanges(), 
	excludeFusionReads=FALSE,
	loadLimitRangesReads=FALSE, ...)

Arguments

bamFileYieldSize	Maximum number of paired Reads in the temprorary files created as the result of dividing the input .bam file.
bamFile	Path of the input bam file.
isPaired	Whether the bam file is the result of a paired end sequencing read mapping (TRUE) or not (FALSE).
isPairedDuplicate	Whether extract only (if set TRUE), filter (FALSE) or include (if set NA) PCR dupplicates for paired mapped reads. It uses the FLAG field in the bam file to filter the duplicate read. If the mapping software does not support detection and flaging the duplicate reads dedup tool of BamUtil or MarkDuplicates of Picard tools could be used.
isSingleReadDuplicate	Whether extract only (if set TRUE), filter (FALSE) or include (if set NA) PCR dupplicates for single mapped reads.
reference	Dataframe to be used as reference; It should at least contain three same-size vectors with the tag names chr, begin, and end which describe the genome coordinates of the introns and exons. It also accepts a GRanges object as input. To build a new reference check the referencePrepare function.
referenceGeneNames	A vector with the same size as the row-size of the reference which include the gene names.
referenceIntronExon	A vector with the same size as the row-size of the reference with values "intron" and "exon" describing which (intron or exon) each row of the reference represents.
repeatsTableToFilter	A data frame with similar structure as the reference, i.e. includes chr, begin, and end columns. If defined, all reads mapped to the described regions would be ingnored and the Intron/exon lengths would be corrected to exclude the regions with repetetive DNA sequences. See getRepeatTable.
junctionReadsOnly	The parameter is considered if the method is set as IntRet or ExEx (NOT IntSpan). It declares whether only consider the Intron-Exon or Exon-Exon junction reads and ignore the reads that fully map to exons or introns. By default this argument is set as FALSE.
outFile	The name or path of the result file.
logFile	The log file path; if defined log information are written to the log file.
returnObj	If set TRUE in addition to producing result text files, the results would also be returned as an object of class SummarizedExperiment.
method	A vector describing the summarization methods to use; i.e. whether count reads mapping to the introns (IntRet), reads mapping to the exons (ExEx), reads spanning the introns (IntSpan), or reads that skip the exons (ExSkip). In IntSpan mode the introns in the reference are taken into account only; whilst in IntRet the introns and their spanning exons, and in ExEx and ExSkip mode only the exons in the reference are taken into account.
strandSpecific	The description for strand specificity of the RNAseq data. The values are either "unstranded", "stranded", or "reverse".If the reads are not strand specific or directional use "unstranded". If the first read in paired-read sequencing or the reads single-read sequencing is in the same direction as the the transcript strand use "stranded". If the first read in paired-read sequencing or the reads in single-read sequencing is in the oposite direction to the transcript strand use "reverse".
appendLogFile	Whether log information should be appended to the logFile. It is FALSE by default.
sampleName	The name of the sample being analyzed. It will be included in the returned object if returnObj is TRUE.
scaleLength	A vector constructed of TRUE/FALSE values, same size as the method argument. It indcates whether the retention levels of the intron/exons should be scaled to their lengths.
scaleFragment	A vector constructed of TRUE/FALSE values, same size as the method argument. It indcates whether the retention levels of the intron/exons should be scaled to the sum of retention levels (i.e. mapped fragments) over the genes.
limitRanges	A GRanges object. If defined it only loads sequencing read if they fall in the defined coordinates. It is similar to which parameter in ScanBamParam.
excludeFusionReads	Only valid if limitRanges is defined. It filters the defined by limitRanges. It also filters the read pairs if each read pair maps reads pairs where one of the reads either do not fall into one of the regions to a different region defined in limitRanges. It is useful to ignore analyzing the chimeric reads and fusion reads, i.e. reads that map to fusion genes. To filter properly, limitRanges must include coordinates of all genes.
loadLimitRangesReads	Boolean (TRUE/FALSE) variable. If set as TRUE only the reads in the limitRanges are loaded from bam file (and bamFileYieldSize parameter will be ignored).
...	Other parameter settings specific to BamFile-class function in the Rsamtools package. Parameters qnamePrefixEnd and qnameSuffixStart are in particular useful to modify qnames in the BAM files.

Value

If returnObj is set TRUE in addition to making result text files, dependant on whether a single or two method is defined, the results would be returned as a single object of class SummarizedExperiment or as a list of size 2 which includes 2 objects of class SummarizedExperiment one for IntRet and the other for ExEx.

Author(s)

Ali Oghabian

See Also

interest.

Examples

# Creating temp directory to store the results
outDir<- file.path(tempdir(),"interestFolder")
dir.create(outDir)
outDir<- normalizePath(outDir)

# Loading suitable bam file
bamF <- system.file("extdata", "small_test_SRR1691637_ZRSR2Mut_RHBDD3.bam", 
	package="IntEREst", mustWork=TRUE)


# Choosing reference for the gene RHBDD3
ref=u12[u12[,"gene_name"]=="RHBDD3",]

test= interest.sequential(
	bamFileYieldSize=10000,
	bamFile=bamF,
	isPaired=TRUE,
	isPairedDuplicate=FALSE,
	isSingleReadDuplicate=NA,
	reference=ref,
	referenceGeneNames=ref[,"ens_gene_id"],
	referenceIntronExon=ref[,"int_ex"],
	repeatsTableToFilter=c(),
	outFile=paste(outDir,
	    "interestRes.tsv", sep="/"),
	logFile=paste(outDir, 
	    "log.txt", sep="/"),
	method=c("IntRet","IntSpan"),
	strandSpecific="unstranded",
	returnObj=TRUE, 
	scaleLength= c(TRUE,FALSE), 
	scaleFragment= c(TRUE,TRUE)
)

test

gacatag/IntEREst documentation built on July 29, 2024, 1:12 a.m.