OverlapEncodings-class {IRanges}R Documentation

OverlapEncodings objects

Description

The OverlapEncodings class is a container for storing the "overlap encodings" returned by the encodeOverlaps function.

Usage

## OverlapEncodings accessors:

## S4 method for signature 'OverlapEncodings'
length(x)
## S4 method for signature 'OverlapEncodings'
Loffset(x)
## S4 method for signature 'OverlapEncodings'
Roffset(x)
## S4 method for signature 'OverlapEncodings'
encoding(x)
## S4 method for signature 'OverlapEncodings'
levels(x)
## S4 method for signature 'OverlapEncodings'
flippedQuery(x)

## S4 method for signature 'OverlapEncodings'
Lencoding(x)
## S4 method for signature 'OverlapEncodings'
Rencoding(x)

## S4 method for signature 'OverlapEncodings'
ngap(x)
## S4 method for signature 'OverlapEncodings'
Lngap(x)
## S4 method for signature 'OverlapEncodings'
Rngap(x)

## Coercing an OverlapEncodings object:

## S4 method for signature 'OverlapEncodings'
as.data.frame(x, row.names=NULL, optional=FALSE, ...)

## Low-level related utilities:

## S4 method for signature 'character'
Lencoding(x)
## S4 method for signature 'character'
Rencoding(x)
## S4 method for signature 'character'
ngap(x)
## S4 method for signature 'character'
Lngap(x)
## S4 method for signature 'character'
Rngap(x)

## S4 method for signature 'factor'
Lencoding(x)
## S4 method for signature 'factor'
Rencoding(x)
## S4 method for signature 'factor'
ngap(x)
## S4 method for signature 'factor'
Lngap(x)
## S4 method for signature 'factor'
Rngap(x)

Arguments

x

An OverlapEncodings object. For the low-level utilities, x can also be a character vector or factor containing encodings.

row.names

NULL or a character vector.

optional, ...

Ignored.

Details

Given a query and a subject of the same length, both list-like objects with top-level elements typically containing multiple ranges (e.g. RangesList objects), the "overlap encoding" of the i-th element in query and i-th element in subject is a character string describing how the ranges in query[[i]] are qualitatively positioned relatively to the ranges in subject[[i]].

The encodeOverlaps function computes those overlap encodings and returns them in an OverlapEncodings object of the same length as query and subject.

The topic of working with overlap encodings is covered in details in the "Overlap encodings" vignette in the GenomicRanges package.

OverlapEncodings accessors

In the following code snippets, x is an OverlapEncodings object typically obtained by a call to encodeOverlaps(query, subject).

length(x): Get the number of elements (i.e. encodings) in x. This is equal to length(query) and length(subject).

Loffset(x), Roffset(x): Get the "left offsets" and "right offsets" of the encodings, respectively. Both are integer vectors of the same length as x.

Let's denote Qi = query[[i]], Si = subject[[i]], and [q1,q2] the range covered by Qi i.e. q1 = min(start(Qi)) and q2 = max(end(Qi)), then Loffset(x)[i] is the number L of ranges at the head of Si that are strictly to the left of all the ranges in Qi i.e. L is the greatest value such that end(Si)[k] < q1 - 1 for all k in seq_len(L). Similarly, Roffset(x)[i] is the number R of ranges at the tail of Si that are strictly to the right of all the ranges in Qi i.e. R is the greatest value such that start(Si)[length(Si) + 1 - k] > q2 + 1 for all k in seq_len(L).

encoding(x): Factor of the same length as x where the i-th element is the encoding obtained by comparing each range in Qi with all the ranges in tSi = Si[(1+L):(length(Si)-R)] (tSi stands for "trimmed Si"). More precisely, here is how this encoding is obtained:

  1. All the ranges in Qi are compared with tSi[1], then with tSi[2], etc... At each step (one step per range in tSi), comparing all the ranges in Qi with tSi[k] is done with rangeComparisonCodeToLetter(compare(Qi, tSi[k])). So at each step, we end up with a vector of M single letters (where M is length(Qi)).

  2. Each vector obtained previously (1 vector per range in tSi, all of them of length M) is turned into a single string (called "encoding block") by pasting its individual letters together.

  3. All the encoding blocks (1 per range in tSi) are pasted together into a single long string and separated by colons (":"). An additional colon is prepended to the long string and another one appended to it.

  4. Finally, a special block containing the value of M is prepended to the long string. The final string is the encoding.

levels(x): Equivalent to levels(encoding(x)).

flippedQuery(x): Whether or not the top-level element in query used for computing the encoding was "flipped" before the encoding was computed. Note that this flipping generally affects the "left offset", "right offset", in addition to the encoding itself.

Lencoding(x), Rencoding(x): Extract the "left encodings" and "right encodings" of paired-end encodings.

Paired-end encodings are obtained by encoding paired-end overlaps i.e. overlaps between paired-end reads and transcripts (typically). The difference between a single-end encoding and a paired-end encoding is that all the blocks in the latter contain a "--" separator to mark the separation between the "left encoding" and the "right encoding".

See the "Overlap encodings" vignette in the GenomicRanges package for examples of paired-end encodings.

ngap(x), Lngap(x), Rngap(x): Extract the number of gaps in each encoding by looking at their first block (aka special block). If an element xi in x is a paired-end encoding, then Lngap(xi), Rngap(xi), and ngap(xi), return ngap(Lencoding(xi)), ngap(Rencoding(xi)), and Lngap(xi) + Rngap(xi), respectively.

Coercing an OverlapEncodings object

In the following code snippets, x is an OverlapEncodings object.

as.data.frame(x): Return x as a data frame with columns "Loffset", "Roffset" and "encoding".

Author(s)

H. Pages

See Also

Examples

example(encodeOverlaps)  # to make 'ovenc'

length(ovenc)
Loffset(ovenc)
Roffset(ovenc)
encoding(ovenc)
levels(ovenc)
nlevels(ovenc)
flippedQuery(ovenc)
ngap(ovenc)

as.data.frame(ovenc)
ngap(levels(ovenc))

[Package IRanges version 1.18.2 Index]