A class for representing a list of high throughput Chromosome Conformation Capture data from next-generation sequencing experiments.
signature("HTClist") is composed of a list of contact maps,
representing the chromosomal interactions between pair of
The expected number of maps for a complete
signature("HTClist") object should be equal to
'lchrs+(lchrs*(lchrs-1)/2)'. In this case, the chr1-chr2 map is stored
once, but the dataset is complete.
signature("HTClist") object is composed of all pairwise
interaction maps, it means that the chr1-chr2 AND the chr2-chr1 maps
will be stored. This way of storing the data is less memory efficient
but can ease the use of some genome-wide algorithm.
Note that the
getCombinedContact method should be used
carefully. This method merges all single contact maps in one
genome-wide map, therefore creating a very big matrix requiring memory
space. However, this method is useful for many genome-wide analysis.
normPerExpected method applied to HTClist object is only
available with the 'mean' method (see
details). In this case, the mean counts per distance are calculated
over all intra-chromosomal maps.
HTClist represents a list of
HTCexp objects and can
be created as follow :
HTClist(...) : Creates a HTClist object using HTCexp objects supplied in '...'
signature("HTClist") object 'x'
objects in '...'. The results is an object of class
signature("HTClist"): a more
detailed output of the experiment than provided by
all the pairwise contact maps
half of the pairwise contact maps
Logical; true if 'x' contains all intra and interchromosomal maps
Logical; true if 'x' contains all interchromosomal pairs, i.e. chr1chr2 and chr2chr1
applies 'isBinned' to each element in 'x'
applies 'isIntraChrom' to each element in 'x'
merge all contact maps in a single big matrix
merge all x and y intervals in single GRangesList object, or in a single GRanges object if merge=TRUE
normalized by genomic distance all intra-chromosomal maps. See details
applies 'range' to each element in 'x'
return the reduce range of all elements in 'x'
reduce a HTClist object to the list of provided chromosomes. Intra/Interchromosomal maps are returned accoring to the cis and trans args. If extend = True, all maps involving one of the chromosomes are returned
return the sequence levels of all elements in 'x'
coercion to simple
get the names of the elements
summarized output of the experiment, with informations about the data dimension
return descriptive summary statistics for each interaction map
x. Can be the
positional index or its name.
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