HTClist-class {HiTC} | R Documentation

## Class 'HTClist'

### Description

A class for representing a list of high throughput Chromosome Conformation Capture data from next-generation sequencing experiments.

### Details

A `signature("HTClist")` is composed of a list of contact maps, representing the chromosomal interactions between pair of chromosomes.
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.
If a `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. The `normPerExpected` method applied to HTClist object is only available with the 'mean' method (see `getExpectedCounts` for details). In this case, the mean counts per distance are calculated over all intra-chromosomal maps.

### Constructor

The `HTClist` represents a list of `HTCexp` objects and can be created as follow :

  `HTClist(...)` : Creates a HTClist object using HTCexp objects supplied in '...'

### Methods

c(x, ...)

  Combines a `signature("HTClist")` object 'x' with `signature("HTClist")` or `signature("HTCexp")` objects in '...'. The results is an object of class `signature("HTCList")`

detail(x)

  `signature("HTClist")`: a more detailed output of the experiment than provided by `show`.

forcePairwise(x)

  return a `signature("HTClist")` with all the pairwise contact maps

forceSymmetric(x)

  return a `signature("HTClist")` with half of the pairwise contact maps

isComplete(x)

  Logical; true if 'x' contains all intra and interchromosomal maps

isPairwise(x)

  Logical; true if 'x' contains all interchromosomal pairs, i.e. chr1chr2 and chr2chr1

isBinned(x)

  applies 'isBinned' to each element in 'x'

isIntraChrom(x)

  applies 'isIntraChrom' to each element in 'x'

getCombinedContacts(x)

  merge all contact maps in a single big matrix

getCombinedIntervals(x, merge=FALSE)

  merge all x and y intervals in single GRangesList object, or in a single GRanges object if merge=TRUE

normPerExpected(x)

  normalized by genomic distance all intra-chromosomal maps. See details

ranges(x)

  applies 'range' to each element in 'x'

range(x)

  return the reduce range of all elements in 'x'

reduce(x, chr, cis=TRUE, trans=TRUE, extend=FALSE)

  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

seqlevels(x)

  return the sequence levels of all elements in 'x'

as.list(x)

  coercion to simple `list` object

names(x)

  get the names of the elements

show(x)

  summarized output of the experiment, with informations about the data dimension

summary(x)

  return descriptive summary statistics for each interaction map

x[i]

  Get elements `i` from `x`. Can be the positional index or its name.

### Author(s)

Nicolas Servant

### See Also

`GRangesList-class`, `HTCexp-class`

### Examples

    exDir <- system.file("extdata", package="HiTC")
    l <- sapply(list.files(exDir, pattern=paste("HIC_gm06690_"), full.names=TRUE),
                import.my5C)
    hiC <- HTClist(l)
    names(hiC)

    ## Methods
    ranges(hiC)
    range(hiC)
    isComplete(hiC)
    isPairwise(hiC)
    isBinned(hiC)
    isIntraChrom(hiC)
    seqlevels(hiC)

[Package HiTC version 1.38.0 Index]