duplicates.barplot: Read duplicates barplot
In TEQC: Quality control for target capture experiments

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

Barplot showing fractions of reads / read pairs which are unique and for which there are two, three, ... copies. Separate bars are made for on- and off-target reads / read pairs

1	duplicates.barplot(reads, targets, returnDups=FALSE, truncateX, col=c("red","lightblue"), xlab, ylab, ylim, ...)

`reads`	`RangedData` table containing positions of sequenced reads, i.e. output from `get.reads`. Alternatively, for paired-end data, it can be the output of `reads2pairs` when multiplicities of read pairs instead of fraction of single reads shall be visualized.
`targets`	`RangedData` table containing positions of target regions, i.e. output from `get.targets`
`returnDups`	if `TRUE`, on- and off-target read / read pair multiplicities are returned
`truncateX`	integer; show bars only up to a read / read pair multiplicity of `truncateX` (x-axis)
`col`	vector specifying the two colors of bars and legend for on- and off-target read multiplicities
`xlab, ylab`	x- and y-axis labels
`ylim`	y-axis coordinate ranges
`...`	further graphical parameters passed to `barplot`

Single-end reads are considered as duplicates if they have same start end end position. Paired-end read pairs are considered as duplicates if start and end positions of both reads of the pairs are identical. Usually, duplicates are removed before further analyses (e.g. SNP detection), because they could represent PCR artefacts. However, in target capture experiments it is likely to have also many "real" duplicates (actual different molecules that happen to start at same position) due to the "enrichment" of the target regions. The separation in the barplot between on- and off-target reads / read pairs gives an impression on whether on-target there are more reads with higher multiplicites, which hence might indicate a reasonable amount of "real" duplication. A paired-end read pair is considered on-target if at least one of its reads overlaps with a target.

Barplot where the bar heights correspond to fractions of reads / read pairs which are present in the data with the respective number of copies (x-axis). Fractions are calculated separately for on- and off-target reads / read pairs. A read pair is considered on-target if at least one of its reads overlaps with a target. Absolute numbers (in millions) are additionally written on top of the bars.

If returnDups equals TRUE, a list with two elements absolute and relative is returned. The former is a matrix that contains the absolute numbers of reads / read pairs for each multiplicity (columns), for both on- and off-target reads / read pairs (rows). The latter gives row-based fractions which correspond to the bar heights.

Manuela Hummel m.hummel@dkfz.de

get.reads, reads2pairs, get.targets

## get reads and targets
exptPath <- system.file("extdata", package="TEQC")
readsfile <- file.path(exptPath, "ExampleSet_Reads.bed")
reads <- get.reads(readsfile, idcol=4, skip=0)
targetsfile <- file.path(exptPath, "ExampleSet_Targets.bed")
targets <- get.targets(targetsfile, skip=0)

## duplicates barplot for single reads
duplicates.barplot(reads, targets, returnDups=TRUE)

## duplicates barplot for read pairs
readpairs <- reads2pairs(reads)
duplicates.barplot(readpairs, targets, returnDups=TRUE)

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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Attaching package: 'Rsamtools'

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Loading required package: hwriter
Warning message:
replacing previous import 'BiocGenerics::path' by 'Rsamtools::path' when loading 'TEQC' 
[1] "read 19546 sequenced reads"
[1] "read 50 (non-overlapping) target regions"
$absolute
               1    2   3   4  5  6 7 8 10
on target   3166 1114 390 153 52 16 7 2  1
off target 11184  262  52  15  3  0 0 0  0

$relative
                   1          2           3           4            5          6
on target  0.6459906 0.22730055 0.079575597 0.031218119 0.0106100796 0.00326464
off target 0.9711705 0.02275096 0.004515457 0.001302536 0.0002605071 0.00000000
                    7          8         10
on target  0.00142828 0.00040808 0.00020404
off target 0.00000000 0.00000000 0.00000000

Warning messages:
1: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData 
2: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData 
Warning messages:
1: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData 
2: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData 
3: The coercion method from list to RangedData is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData 
$absolute
              1   2  3 4
on target  4026 350 28 3
off target 4949   1  0 0

$relative
                   1            2           3            4
on target  0.9135466 0.0794191060 0.006353528 0.0006807352
off target 0.9997980 0.0002020202 0.000000000 0.0000000000

Warning messages:
1: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData 
2: The "lapply" method for RangedData objects is deprecated and won't be
  replaced. Please migrate your code to use GRanges or GRangesList
  objects instead. RangedData objects will be deprecated soon (their use
  has been discouraged since BioC 2.12, that is, since 2014). See
  IMPORTANT NOTE in ?RangedData