selectVDVreads: Select VDV reads from a set of Nanopore reads

In pgpmartin/NanoBAC: Analysis of long read (Oxford Nanopore, PacBio) data from BAC or large plasmid sequencing

Description

The function does the following:

• Selects VDV readsThis is done using FilterBACreads

• Estimate BAC sizeThe size of the insert sequence is estimated using estimateBACsizeFromVDV

• Select VDV reads of the right sizeVDV reads within +/- SizeTolerance% of the estimated size are selected

• Plot VDV read sizeThe plot illustrates the size of all VDV reads and the selection process

By default, if alignment to the host genome is provided in the ReadClass object (column HostAlign), then the selected VDV reads do not align to the host genome. The function allows the user to exclude reads from the analysis.

Usage

selectVDVreads(
  ReadClass = NULL,
  SizeTolerance = 0.05,
  WithGeneA = NULL,
  WithGeneB = NULL,
  ignoredReads = NULL,
  MaxClusters = 10L,
  makePlot = TRUE,
  plotVar = c("ReadLength", "InsertLength")
)

Arguments

ReadClass	Either a tibble obtained with the AnnotateBACreads function or a path to an rds file containing such a file
SizeTolerance	A single number in [0,1[. Reads with a size corresponding to the estimated size +/- SizeTolerance% are selected
WithGeneA	Logical. Should the VDV reads align with GeneA? Default is NULL, i.e. no filtering on GeneA alignment
WithGeneB	Logical. Should the VDV reads align with GeneB? Default is NULL, i.e. no filtering on GeneB alignment
ignoredReads	(optional) vector of read names that should be ignored.
MaxClusters	Integer. Maximum number of clusters to make with VDV reads to estimate the size of the DNA insert. Default to 10 which in our hands works in most situations.
makePlot	Logical. Should a plot be produced (and saved in the result)
plotVar	Character string. Variable to plot: either 'ReadLength' or InsertLength.

Value

A list with the following objects:

• VDVreadsA tibble with info on VDV reads: name, length, selection by the procedure, cluster

• InsertSizeEstimateA list with result from the estimateBACsizeFromVDV function

if makePlot is TRUE, then the list also contains:

• VDVlengthPlotThe plot (ggplot2 object)

• PlotTypeThe variable used to make the plot, i.e. the plotVar argument that was used to create the object

• xcoordThe x coordinates of the points (obtained using geom_jitter) in order to reproduce the plot easily

Author(s)

Pascal GP Martin

Examples

## Path to file (.rds) created with the AnnotateBACreads function
pathRC <- system.file("extdata", "BAC02_ReadClass.rds", package = "NanoBAC")
## Import the data
annotatedReads <- readRDS(pathRC)
## Select VDV reads that contain alignment to GeneA and GeneB
myVDVreads <- selectVDVreads(ReadClass = annotatedReads,
                             WithGeneA = TRUE,
                             WithGeneB = TRUE)
## Same but making less clusters and producing a plot on insert length rather than read length
myVDVreads <- selectVDVreads(ReadClass = annotatedReads,
                             WithGeneA = TRUE,
                             WithGeneB = TRUE,
                             MaxClusters = 8,
                             plotVar = "InsertLength")

pgpmartin/NanoBAC documentation built on Dec. 11, 2020, 9:51 a.m.