make_bg_data: Read a multiple-FEV file to create a background set of...

In palmid: RdRP Analysis Suite

Description

Read a multiple-FEV file to create a background set of palmprints Standard approach is to use palmDB

Usage

make_bg_data(fev.path, dataset.id = NULL, return.data = TRUE)

Arguments

fev.path	Path to multiple fev file
dataset.id	Name for output dataset.
return.data	Boolean. Return data.frame instead of writing file [TRUE]

Value

NULL: will write an RData file to data/<fev.path>.RData

Examples

#' # palmscan example fev file
ps.fev.path <- system.file( "extdata", "waxsys.fev", package = "palmid")
example_bg <- make_bg_data(fev.path = ps.fev.path, dataset.id = 'example_bg')

## Documentation on Making Background Dataset from palmDB
##  i.e. load("palmdb")
## 
## Download palmDB to make background set
# system("git clone https://github.com/rcedgar/palmdb.git")
#
## Generate the palmprint-FEV with palmscan
# system("palmscan -search_pp palmdb/2021-03-02/otu_centroids.fa \
#         -all -rdrp -fevout data/palmdb210302.fev")
#
## Create R object (data.frame)
# make_bg_data(fev.path = "data/palmdb210302.fev",
#              dataset.it = "palmdb",
#              return.data = FALSE)
#
# load("palmdb")

palmid documentation built on Oct. 15, 2021, 9:06 a.m.