DensityContainer-class: Class '"DensityContainer"'

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

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 [e-mail]

See Also

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

Examples

showClass("DensityContainer")

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