tvStats-methods: DensityContainer accessor function

In TransView: Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets

Description

Retrieve important metrics from the outcome of parseReads() stored in class DensityContainer and its super classes.

Usage

## S4 method for signature 'DensityContainer'
tvStats(dc)

Arguments

dc	An object of class DensityContainer.

Value

Returns a list with the slots of the DensityContainer and its super classes. In detail:

• "ex_name": A user provided string to define a name of this dataset

• "origin": Filename of the original file

• "spliced": Should the class be treated like an RNA-Seq experiment for e.g. plotTV?

• "paired": Does the source file contain reads with proper pairs?

• "readthrough_pairs": If TRUE, paired reads will be connected from left to right as one long read.

• "filtered": Is there a range filter in place? If yes, slicing should be only conducted using the same filter!!

• "strands": Which strands were parsed at all. Can be "+", "-" or "both"

• "nreads": Total number of reads

• "coverage": Total coverage computed by total map mass/(chromosome end - chromosome start). Chromosome length derived from the SAM/BAM header

• "maxScore": Maximum read pileup found in file

• "lowqual": Amount of reads that did not pass the quality score set by min_quality or were not mapped

• "paired_reads": Amount of reads having multiple segments in sequencing

• "proper_pairs": Amount of pairs with each segment properly aligned according to the aligner

• "collapsed": If maxDups is in place, the reads at the same position and strand exceeding this value will be counted here.

• "compression": Size of a gap triggering an index event

• "chromosomes": Character string with the chromosomes with reads used for map construction

• "filtered":_reads Amount of reads

• "pos": Reads used from the forward strand

• "neg": Reads used from the reverse strand

• "lcoverage": Local coverage which is computed by filtered map mass/covered region

• "lmaxScore": Maximum score of the density maps

• "size": Size in bytes occupied by the object

Author(s)

Julius Muller [e-mail]

TransView documentation built on Nov. 8, 2020, 5:31 p.m.