paf2gr: Convert an paf file imported with 'read_paf' to a 'GRanges'

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

Description

the ranges in the resulting GRanges object correspond either to the reads or to the target depending on the value of the focus argument

Usage

paf2gr(paf, focus = c("target", "reads"), includetags = TRUE)

Arguments

paf	A tibble with a paf file imported with the read_paf function
focus	Character string. Either "target" or "reads" indicating which ranges will be represented in the GRanges
includetags	Logical. Should the tags in the paf file be present in mcols from the GRanges (default is TRUE)?

Value

a GRanges object

See Also

read_paf

Examples

## Example data set:
    Path2paf <- system.file("extdata", "BAC02_mmap2Ecoli.paf", package = "NanoBAC")
## Import the data (ignore the parsing failures):
   suppressWarnings(mypaf <- read_paf(Path2paf))
## Convert the dataset to a GRanges focusing on the reads
   mypafgr <- paf2gr(mypaf)

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