DensityContainer-class {TransView} | R Documentation

## Class `"DensityContainer"`

### Description

Container with the pointer of the actual density maps and a histogram. Inherits from internal classes storing informations about the origin and the details of the results.

### Objects from the Class

Objects are created by the function `parseReads()` using an internal constructor.

### Accessors

dc represents a `"DensityContainer"` instance in the following

`data_pointer(dc)`:

  A character string pointing to the read density map. It points to a variable in .GlobalEnv which is essentially a list resulting from a call to `parseReads`. The storage space can be freed with the `rmTV` function.

`ex_name(dc)`,`ex_name(dc)<-value`:

  Get or set a string to define a name of this data set

`origin(dc)`:

  Filename of the original file

`histogram(dc)`:

  A histogram of read pile-ups generated across all read density maps after filtering excluding gaps.

`env(dc)`:

  The environment which holds the data_pointer target.

`spliced(dc)`,`spliced(dc)<-bool`:

  This option will mark the object to be treated like a data set with spliced reads.

`readthrough_pairs(dc)`:

  If TRUE, paired reads will be connected from left to right and used as one long read.

`paired(dc)`:

  Does the source file contain reads with proper pairs?

`filtered(dc)`:

  Is there a range filter in place? If `TRUE`, slicing should be only conducted using the same filter!!

`strands(dc)`:

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

`filtered_reads(dc)`:

  FilteredReads class storing information about reads used for read density construction

`chromosomes(dc)`:

  Character string with the chromosomes used for map construction

`pos(dc)`:

  Reads used from the forward strand

`neg(dc)`:

  Reads used from the reverse strand

`lsize(dc)`:

  Total region covered by reads within the densities returned

`gsize(dc)`:

  Equals to the sum of the length of all ranges from 0 to the last read per chromosome within the chromosome.

`lcoverage(dc)`:

  Local coverage within the densities returned which is computed by local mapmass/lsize

`lmaxScore(dc)`:

  Maximum read pileup within the density maps after filtering

`fmapmass(dc)`:

  Total map mass after quality filtering present in the file. Equals to filtered_reads*read length

`nreads(dc)`:

  Total number of reads in the file.

`coverage(dc)`:

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

`maxScore(dc)`:

  Maximum read pileup found in file after quality filtering

`lowqual(dc)`:

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

`paired_reads(dc)`:

  Amount of reads having multiple segments in sequencing

`proper_pairs(dc)`:

  Amount of pairs with each segment properly aligned according to the aligner

`collapsed(dc)`:

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

`size(dc)`:

  Size in bytes occupied by the object.

### Slice Methods

slice1

  `signature(dc = "DensityContainer")`: Fetch a slice of read densities.

slice1T

  `signature(dc = "DensityContainer")`: Recover the structure of a gene from a provided pre-processed GTF and read densities.

sliceN

  `signature(dc = "DensityContainer", ranges = "data.frame")`: Like slice1 but optimized for repeated slicing.

sliceNT

  `signature(dc = "DensityContainer", tnames = "character", gtf = "data.frame")`: Like slice1T but optimized for repeated slicing.

### Convenience Methods

tvStats

  `signature(dc = "DensityContainer")`: Returns a list of important metrics about the source file.

### Extends

Class `TransView`, directly.

### Note

Class TotalReads and FilteredReads are not exported but their slots can be fully accessed by several accessors and the `tvStats()` method.

### Author(s)

Julius Muller ju-mu@alumni.ethz.ch

### See Also

`tvStats-methods`, `slice1-methods`, `sliceN-methods`, `histogram-methods`, `rmTV-methods`

### Examples

    showClass("DensityContainer")

[Package TransView version 1.26.1 Index]