deprecated {ShortRead}R Documentation

Deprecated and defunct functions

Description

These functions were introduced but are now deprecated or defunct.

Usage

basePath(object, ...)
pileup(start, fraglength, chrlength, dir = strand( "+" ),
       readlength = fraglength, offset = 1)

Arguments

object

For basePath, and object of class ExperimentPath.

...

Additional arguments.

start

A vector with the start positions of each read on the reference sequence. All reads must correspond to the same reference sequence.

fraglength

A vector of the same length as 'start' with the lengths of all the fragments. Alternatively, a single integer, specifying one constant length to assume for all tags.

chrlength

The length of the reference sequence. You may use the function readBfaToc to extract this information from the .bfa file.

dir

A factor with level "-" and "+" of the same length as 'start', specifying whether the fragment extends to the right (towards higher index values, '+') or to the left (towards lower index values, '-') beyond the read. See below for more explanation.

readlength

The length of the reads, either as a vector of the same length as 'start' or as a single number. This parameter makes sense only if 'dir' is used, too. If not specified, read lengths and fragment lengths are taken to be the same.

offset

The index of the first base pair in the result vector. The default is 1, i.e. assumes that the 'start' positions are in 1-based chromosome coordinates.

Value

pileup

an integer vector of length 'chrlength', each element counting how many fragments map to this basepair.

Note

(the following refers to the pileup function)

1. This function is not suitable for paired-end reads.

2. If the arguments 'dir' and 'readlength' are not used, the fragments are assumed to start at the positions given in 'start' and extend to the right by the number of basepairs given in fraglength. If 'dir' and 'readlength' are supplied then the interval starting at 'start' and extending to the right by the number of base pairs given in 'readlength' marks the position of the read, which is one end of the fragment. If 'dir' ist '+', it is taken as the left end and the fragment will be extended to the right to have the total length given by 'fraglength'. If 'dir' is '-', the end is taken as the right end and is extended to the left. Note that in the latter case, the 'start' position does mark the border between read and rest of fragment, not an actual 'end' of the fragment. If you are confused now, look at the examples below.

3. Sorry for the inconsequent use of 'width' and 'length' in a seemingly interchangeable fashion.

Author(s)

Simon Anders, EMBL-EBI, sanders@fs.tum.de

Examples

## Not run:  
Example 1: Assuming that 'lane' is an 'AlignedRead' object containing
aligned reads from a Solexa lane, you may get a pile-up representation
of chromosome 13 as follows

chr13length <- 114142980   # the length of human chromosme 13
pu <- pileup(position(lane)[chromosome(lane)=="13"],
             width(lane), chr13length )

Example 2: Even though the width of the reads (as repored by
'width(lane)') is only 24, these 24 bp are just one end of a longer
fragment. Assuming that all fragments have been sonicated to about the
same length, say 150 bp, we may get a better pile-up representation by:

pu2 <- pileup(position(lane)[chromosome(lane)=="13"], 150,
              chr13length, strand(lane)[chromosome(lane)=="13"],
              width(lane) )

## End(Not run)

[Package ShortRead version 1.12.4 Index]