FilterBACreads: Select specific reads from a table of BAC read annotations...

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

Description

Select specific reads from a table of BAC read annotations obtained by the function AnnotateBACreads

Usage

FilterBACreads(
  ReadClass = NULL,
  readtype = "VDV",
  MinReadLength = NULL,
  alnGeneA = NULL,
  alnGeneB = NULL,
  isHostAlign = NULL,
  VDVInsertLengthTarget = NULL,
  VDVInsertLengthTolerance = 0.05
)

Arguments

ReadClass	Either a tibble obtained with the AnnotateBACreads function or a path to an RDS file containing such a tibble
readtype	Character vector. Type(s) of reads to select. Values should be in c("VDV", "DVD", "VD", "D", "V", "Chimeric", NA). (Defaults to "VDV")
MinReadLength	Integer. Minimum length of the selected reads. Reads below this length are dropped. (defaults to NULL, i.e. no filtering on read length)
alnGeneA	Logical. Should the selected read align to GeneA ? (defaults to NULL, i.e no filtering on GeneA alignment)
alnGeneB	Logical. Should the selected read align to GeneB ? (defaults to NULL, i.e no filtering on GeneB alignment)
isHostAlign	Logical. Should the selected reads align to the host genome (TRUE) or not (FALSE)? (defaults to NULL, i.e no filtering on host genome alignment alignment)
VDVInsertLengthTarget	Integer. What is the estimated length of the DNA insert (without the vector) in the VDV reads to be selected? (Defaults to NULL, no filtering on VDV read length)
VDVInsertLengthTolerance	Numeric. Number in [0,1[. What tolerance (in %) is accepted around VDVInsertLengthTarget?

Details

The function uses the column "LongestDNA" to filter for the size of VDV reads

Value

tibble with selected reads.

Examples

## Path to file (.rds) created with the AnnotateBACreads function
pathRC <- system.file("extdata", "BAC02_ReadClass.rds", package = "NanoBAC")
## Extract the annotation of all VDV reads longer than 111 kb
FilterBACreads(pathRC, "VDV", 111e3)
## Extract the annotation of the VDV reads which have an insert that is 104 kb long (+/- 0.1%)
FilterBACreads(pathRC, "VDV",
               VDVInsertLengthTarget = 104e3,
               VDVInsertLengthTolerance = 0.001)
## Extract the annotation of the D reads that map to the E. coli genome
FilterBACreads(pathRC, "D", isHostAlign = TRUE)
## Extract the annotation of the VD and the VDV reads that align to both GeneA and GeneB
FilterBACreads(pathRC, c("VD", "VDV"), alnGeneA = TRUE, alnGeneB = TRUE)
## There are no VDV reads that align to the E. coli host genome
## Not run: 
FilterBACreads(pathRC, "VDV", isHostAlign = TRUE)

## End(Not run)

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