blaST2GR: Convert an imported blast result table to a GRanges

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

Description

Note that readlength table is expected to contain all reads (not only the reads that have an alignment)

Usage

blaST2GR(blastresults, readlength)

Arguments

blastresults	A tibble obtained with the readBlast function (containing strand info)
readlength	A tibble with 2 columns named ReadName and ReadLength. This table is expected to contain all reads, not only those having an alignment to the vector

Value

GRanges

Examples

## Import some blast result data:
    Path2Blast <- system.file("extdata", "BAC02_Blast18S.res", package = "NanoBAC")
    myblastResult <- readBlast(Path2Blast)
## Import a 2-column table with ReadName and ReadLength:
    Path2ReadLength <- system.file("extdata", "BAC02_ReadLength.tsv", package = "NanoBAC")
    ReadLengthTable <- read.table(Path2ReadLength,
                                  sep = "\t", header = FALSE,
                                  stringsAsFactors = FALSE,
                                  col.names = c("ReadName", "ReadLength"))
## Convert the blast result table to a GRanges
    myBlastGR <- blaST2GR(myblastResult, ReadLengthTable)

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