writeAmp: Writes amplicon data to MMDIT

In Ahhgust/MMDIT: Mitochondrial mixture project

Description

this loads in amplicon data (i.e., the coordinates of the amps) into the MITO db. If the alignments were to a modified reference (duplicating bits to accommodate circular alignment) this routine converts those back to the original units. thus the last amplicon may "wrap around" (eg., 16541-80 is a valid locus)

Usage

writeAmp(db, ampFile, kitName, sep = "\t", append = TRUE)

Arguments

db	(the database connection)
ampFile	(a BED file of amplicons; columns 2 and 3 are used only)
kitName	(the NAME of the kit that this corresponds to (e.g., PrecisionID) )
sep	(\"\t\" for a tab-separated file. Anything else is a little wacky... no longer a bed file)
append	(whether or not the amplicons are APPENDED to the list of current amplicons; set to FALSE to overwrite)

Value

the database handle (not necessary to keep this)

Examples

# One way to add another kit:
## Not run: 
# loadAmpData(db, "data/Mybedfile.bed", kit="SomeOtherKit", append=TRUE)

## End(Not run)

Ahhgust/MMDIT documentation built on Jan. 27, 2021, 11:48 a.m.