checkBlastVar: Check if an object was imported using 'readBlast' or import...

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

Description

Check if an object was imported using readBlast or import an object using readBlast

Usage

checkBlastVar(bvar, bform = "outfmt6")

Arguments

bvar	either a path to a Blast result table (gerenated with outfmt=6) or such a table imported with the readBlast function
bform	character string. Currently can only be "outfmt6"

Value

a Blast result table imported with the readBlast function

Examples

## Not run: 
## Create a basic data frame with the right columns
df <- data.frame("QueryACC" = "MyVector",
                 "SubjectACC" = "Read1",
                 "PercentID" = "97.5",
                 "AlnLength" = 2530,
                 "NumMismatch" = 20,
                 "NumGapOpen" = 30,
                 "QueryStart" = 1,
                 "QueryEnd" = 2500,
                 "SubjectStart" = 102490,
                 "SubjectEnd" = 100000,
                 "evalue" = 0.0,
                 "bitscore" = 3000,
                 "Strand")
## checkBlastVar returns the object itself
mytab <- checkBlastVar(df)
## If we mofidy a column name
colnames(df)[1] <- "newcolname"
## then checkBlastVar throws an error
\dontrun{
mytab <- checkBlastVar(df)
}

## End(Not run)

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