ContigLink-method: Estimate Insert size library from pairs of sequence mapping...

In jos4uke/contigLink: What the package does (short line)

Description

Estimate Insert size library from pairs of sequence mapping on the same contig.

Estimate Insert size library from pairs of sequence mapping on two different contigs.

Estimate the assembly quality

Count the number of pairs of sequence that connect two contigs.

Plot method for the class ContigLinkViewer

Usage

## S4 method for signature 'ContigLinkViewer'
EstimateInsertSizeFromSame(object, ...)

## S4 method for signature 'ContigLinkViewer'
EstimateInsertSizeFromDiff(object, ...)

## S4 method for signature 'ContigLinkViewer'
EstimateAssQual(object, EstimateCutOff = TRUE,
  Min = NA, Max = NA, SdNumber = NA)

## S4 method for signature 'ContigLinkViewer'
ContigLinkCount(object, MinCount)

## S4 method for signature 'ContigLinkViewer'
plot(object, x = NA, ...)

Arguments

object	An object of class ContigLinkViewer
An	object of class ContigLinkViewer
object	An object of class ContigLinkViewer
EstimateCutOff	If TRUE, the interval for the insert size is [MeanIsize-(SdNumber*SdIsize), MeanIsize+(SdNumber*SdIsize)]
Min	If EstimateCutOff is FALSE The min value for the insert Size
Max	If EstimateCutOff is FALSE The max value for the insert Size
SdNumber	The number of sd to keep for computing the insert size interval.
An	object of class ContigLinkViewer
MinCount	The minimum number of pairs connecting two contigs
object	An object of class ContigLinkViewer
...	Arguments to be passed to methods, such as graphical parameters (see par). Many methods will accept the following arguments: type what type of plot should be drawn. Possible types are "p" for points, "l" for lines, "b" for both, "c" for the lines part alone of "b", "o" for both ‘overplotted’, "h" for ‘histogram’ like (or ‘high-density’) vertical lines, "s" for stair steps, "S" for other steps, see ‘Details’ below, "n" for no plotting. All other types give a warning or an error; using, e.g., type = "punkte" being equivalent to type = "p" for S compatibility. Note that some methods, e.g. plot.factor, do not accept this. main an overall title for the plot: see title. sub a sub title for the plot: see title. xlab a title for the x axis: see title. ylab a title for the y axis: see title. asp the y/x aspect ratio, see plot.window.
x	the coordinates of points in the plot. Alternatively, a single plotting structure, function or any R object with a plot method can be provided.

Details

Estimate Insert size library from pairs of sequence mapping on the same contig and having the good orientation. The well mapped paired-end sequence (-> <-) belong to this two categorism:

• 1 The strand of the first sequence in pair is + and its sam flag is 99. The strand of the second sequence in the pair is - and its flag is 147. The insert size is obtained by substracting the start position of the first sequence on the contig to the end position of the second sequence on the contig and by adding 1.

• 2 The strand of the first sequence in pair is - and its sam flag is 83. The strand of the second sequence in the pair is + and its flag is 163. The insert size is obtained by substracting the start position of the second sequence on the contig to the end position of the first sequence on the contig and by adding 1.

Estimate Insert size library from pairs of sequence mapping on two contigs. In this case the orientation of the sequence on the contig does not matter. To obtain the insert size, two cases:

• The sequence is the first in the pair The insert size is the length of the first contig plus the end position of the second sequence on the second contig minus the start position of the first sequence on the first contig minus 1.

• The sequence is the second in the pair The insert size is the length of the first contig plus the end position of the first sequence on the first contig minus the start position of the second sequence on the second contig minus 1.

This method creates the AssQual slot which contain 4 objects:

• parameters A vector giving the insert size parameters which will be used to estimate the assembly quality. Min and Max or Mean and sd.

• dfSameQualAssByContig A data.frame summarizing the repartition of the pairs according to the insert size range and the orientation of the pairs. This data.frame has 6 columns:

  • seqnames.1 A vector giving the name of the contig

  • strand.1 A vector giving the mapping strand of the first sequence in pair

  • strand.2 A vector giving the mapping strand of the second sequence in pair

  • outof A vector giving the number of pair that are outside the confidence interval for the insert size

  • nonav A vector giving the number of pair for which the insert size can not be computed

  • within A vector giving the number of pair with an insert size inside the confifence interval

• dfSameQualAssTot A data.frame which sum the dfSameQualAssByContig by orientation only disregarding contig information.

• dfDiffQualAssByContig A data.frame summarizing the repartition of the pairs according to the insert size range and the orientation of the contigs that are linked. This data.frame has 6 columns: for the insert size

• seqnames.1 A vector giving the name of the first contig

• seqnames.2 A vector giving the name of the second contig

• Ori1 A vector giving the orientation of the first contig

• Ori2 A vector giving the orientation of the second contig

• outof A vector giving the number of pair that are outside the confidence interval for the insert size

• within A vector giving the number of pair with an insert size inside the confifence interval

To get the quality, a confident interval has to be computed for the insert size.

This method creates the CLC slot which is a list of 2 objects:

• MinCount A vector giving the minimum number of pairs binding two contigs

• CLC A data.frame with 5 columns giving the number of pairs above the MinCount parameter that support the connection beween two contigs.

  • seqnames.1 A vector giving the name of the first contig

  • seqnames.2 A vector giving the name of the second contig

  • Ori1 A vector giving the orientation of the first contig

  • Ori2 A vector giving the orientation of the second contig

  • within A vector giving the number of pairs above the MinCount parameter that support the connection beween the two contigs.

This plot function allow to generate a graph to vizualize the contigs and their link using the Rgraphviz package. Contigs are the nodes and the number of pairs supporting the link between two are specified by the edge. The ContigLinkViewer object has to be complete.

Author(s)

Delphine Charif & Joseph Tran

Delphine Charif & Joseph Tran

Delphine Charif & Joseph Tran

Delphine Charif & Joseph Tran

Delphine Charif & Joseph Tran

jos4uke/contigLink documentation built on May 19, 2019, 8:44 p.m.