tvStats-methods {TransView} | R Documentation

## DensityContainer accessor function

### 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 ju-mu@alumni.ethz.ch

[Package TransView version 1.30.0 Index]