viewCoverage-methods: viewCoverage

In sheng-liu/SeqData: A data structure and four simple tools build upon it for sequencing data analysis

Description

Generate a bigWig file for viewing read coverage in a genome browser, or a coverageTable.csv for genomic ranges specified.

Usage

#not working
viewCoverage(obj=NULL,obj.control=NULL, bamFile=character(0),bamFile.control=character(0),weight.control=1,feature=character(0),ranges=GRanges(),annotationFile=character(0),split.metaData=F,bigWig=F,smooth=T,description=character(0))

Arguments

obj	A SeqData object.
obj.control	Optional. A SeqData object used as a control to see differential coverage with obj.
bamFile	The full path to the sequencing data. The data needs to be in bam file format.
bamFile.control	Optional. A bam file used as a control to see differential coverage with bam file.
weight.control	A parameter used to weight control data (obj.control or bamFile.control).
feature	interal feature annotation data set, includes: feature=c("gene","erv","repeats","transposon")
ranges	GRanges object specifying the ranges the coverageTable will produce.
annotationFile	csv annotation file for specifying ranges of interest. It must includes the miminum five field: 'chrom','txSart','txEnd','strand' and 'name'.
split.metaData	information in GRanges,or annotation file other than 'chrom','txSart','txEnd','strand' are treated as metaData. if split.metaData=T, the ranges will be splited based on the first column of metaData, and the coverage will be calculated as the total coverage on all ranges that have the same metaData. It can be used in conjunction with parameter "feature","ranges" and "annotationFile".
bigWig	a switch for output bigWig file. The data is from readCoverage slot of SeqData.
description	Optional. User can input short desciption for the output file, it will show up in the file name of the output file.

Details

Generate bigWig file from a bam file for viewing read coverage in a genome browser; it can also generate coverage views on any ranges specified, output as a coverageTable.csv file. coverageTable containing read maxPosition, maxHeight, coverageSums at specific genomic ranges. It also set readCoverage slot, and coverageView slot if ranges are provided.

Note, parameter 'feature','ranges','annotationFile' or 'slit.metaData' are used only with single SeqData/bamFile.

Value

• bamFileName.bigWig a bigWig file for viewing the coverage of the bamFile provided

• bamFileName.csv a csv file contains the coverage information about the GRanges provided.

• coverageView slot if ranges are passed in, a RleViews object are returned and coverage corresponding to each of those ranges are stored in the coverageView slot.

Usage

viewCoverage(obj=NULL,obj.control=NULL,

bamFile=character(0),bamFile.control=character(0),weight.control=1,

feature=character(0),ranges=GRanges(),annotationFile=character(0),

split.metaData=F,bigWig=F,smooth=T,description=character(0))

Note

Parameter 'feature','ranges','annotationFile' or 'slit.metaData' are used only with single SeqData/bamFile.

Examples

# viewCoverage(obj)
# viewCoverage(obj,ranges=GRanges)
# viewCoverage(obj,annotationFile=annotationFile)

# viewCoverage(bamFile=bamFile)
# viewCoverage(bamFile=bamFile,ranges=GRanges)
# viewCoverage(bamFile=bamFile,annotationFile=annotationFile)

# viewCoverage(obj,obj.control)
# viewCoverage(bamFile,bamFile.control)
# to view coverageView slot
# coverageView(obj)[[1]]
# viewCoverage(obj,feature="transposon",split.metaData=T,description="obj_transposon")

sheng-liu/SeqData documentation built on May 29, 2019, 9:22 p.m.