Description Objects from the Class Accessors Slice Methods Convenience Methods Extends Note Author(s) See Also Examples
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 are created by the function parseReads()
using an internal constructor.
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.
signature(dc = "DensityContainer")
: Fetch a slice of read densities.
signature(dc = "DensityContainer")
: Recover the structure of a gene from a provided pre-processed GTF and read densities.
signature(dc = "DensityContainer", ranges = "data.frame")
: Like slice1 but optimized for repeated slicing.
signature(dc = "DensityContainer", tnames = "character", gtf = "data.frame")
: Like slice1T but optimized for repeated slicing.
signature(dc = "DensityContainer")
: Returns a list of important metrics about the source file.
Class TransView
, directly.
Class TotalReads and FilteredReads are not exported but their slots can be fully accessed by several accessors and the tvStats()
method.
Julius Muller ju-mu@alumni.ethz.ch
tvStats-methods
,
slice1-methods
,
sliceN-methods
,
histogram-methods
,
rmTV-methods
1 | showClass("DensityContainer")
|
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