reads2pairs: Merges reads to read pairs
In hummelma/TEQC: Quality control for target capture experiments

Description Usage Arguments Details Value Author(s) See Also Examples

Combines the two reads of a read pair (in case of paired-end data) to a new 'range' starting at the first reads's start position and ending at the second read's end position.

1	reads2pairs(reads, max.distance)

reads

RangedData table containing positions of sequenced reads, i.e. output of get.reads. The first 'values' column has to contain read pair identifiers, i.e. when reads was created by get.reads, the option idcol had to be specified. The input can also contain single reads without 'read mate' (e.g. when the first read of a pair did not align to the reference genome, however the second one did align and was still kept). Those single reads will be returned in a separate table singleReads. When the two reads in a pair align to different chromosomes, they will also be returned in table singleReads.

max.distance

Integer value defining the maximum allowed distance between two reads of a pair (from start position of first read to end position of second read). Reads exceeding this distance will be returned in the separate table singleReads. If max.distance is not specified, reads will be joined to pairs regardless of their distance. Only when the two reads in a pair align to different chromosomes, they will be removed in any case and added to table singleReads.

The function puts together the two reads of each pair and creates new ranges spanning both reads and everything in between. Those ranges correspond to the extent of the actual DNA molecules for which both ends were sequenced. The output of the function can be used by several other functions, whenever calculations should be based on read pairs rather than on single reads, e.g. fraction.reads.target, readsPerTarget, duplicates.barplot

If reads only contains complete read pairs and for all pairs the respective reads align to the same chromosome and their distances do not exceed max.distance (if specified), a RangedData object is returned containing positions of the merged reads per pair, ranging from start position of the first read to end position of the second read.

If reads also contains single reads, or if reads within a pair are further apart than max.distance (if specified) or align to different chromosome, a list is returned with elements

`singleReads`	`RangedData` object containing original positions of single reads without 'read mates' and/or read pairs aligning too far apart or on different chromosomes
`readpairs`	`RangedData` object containing positions of the merged reads per pair, ranging from start position of the first read to end position of the second read

Manuela Hummel m.hummel@dkfz.de

get.reads, fraction.reads.target, readsPerTarget, duplicates.barplot, insert.size.hist

exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
readpairs <- reads2pairs(reads)