alignToWig: Add BAM Alignments to Wiggle Track data objects.

In robertdouglasmorrison/DuffyNGS: Duffy Lab NGS Analysis Pipeline for RNA-seq, DNA-seq, ChIP-seq, and RIP-seq

Add BAM Alignments to Wiggle Track data objects.

Description

Lower level function that adds alignments to wiggle tracks of read pileups for one sample.

Usage

alignToWig( filein, reload = TRUE, annotationFile = "Annotation.txt", optionsFile = "Options.txt", 
	results.path = NULL, dataType = "RNA-seq", readSense = "sense",  maxReads = NULL,
	readBufferSize = 1000000)

Arguments

filein	The name of one sorted BAM file.
reload	Ligical. Should a new empty wiggle track data structure be created, or if FALSE add to an existing wiggle track data structure.
annotationFile	File of sample annotation details, which specifies all needed sample-specific information about the samples under study. See DuffyNGS_Annotation.
optionsFile	File of processing options, which specifies all processing parameters that are not sample specific. See DuffyNGS_Options.
results.path	The top level folder path for writing result files to. By default, read from the Options file entry 'results.path'.
dataType	The type of read data contained in the aligned BAM file.
readSense	One of "sense" or "antisense". Controls the behavior of how alignments are assigned to the strands.
maxReads	Optional integer. Sets a maximum count for how many alignments will be loaded from this BAM file.
readBufferSize	Integer. Sets the buffer sizer for reading in alignments in efficient chunks.

Details

This low level function is called repeatedly to combine genomic and splice BAM files.

Value

A family of binary .WIG files is written to the wig subfolder. Also the function returns an integer giving the number of buffers of alignments that it processed, where zero denotes an error.

Author(s)

Bob Morrison

See Also

pipe.AlignToWig for the high level pipeline step that invokes this function.

robertdouglasmorrison/DuffyNGS documentation built on March 24, 2024, 4:16 p.m.