toxbootmc: Filter and multicore wrapper for 'toxboot'

In toxboot: Bootstrap Methods for 'ToxCast' High Throughput Screening Data

Description

toxbootmc calculates bootstrapped curves for multiple m4ids using mclapply to perform the calculation on many cores.

Usage

toxbootmc(dat, m4ids = NULL, filter = TRUE, boot_method = "smooth",
  cores = 1L, destination = "memory", ...)

Arguments

dat	data.table returned from toxbootQueryToxCast
m4ids	list of m4ids to perform bootstrap calculation. By default NULL, which will run on all m4ids in the in dat.
filter	logical, default TRUE. If TRUE dat will be filtered to remove m4ids that are already in the mongoDB. Ignored if destination is not "mongo".
boot_method	parameter passed to toxboot. Used also if filter is TRUE.
cores	integer length 1, number of cores to supply as mc.cores to mclapply. By default set to 1L which will work on all systems including Windows. Increase to the number of cores on your system (see detectCores) to perform calculations in parallel.
destination	string length 1, options are "mongo", "mysql", "file", "memory"
...	parameters passed to toxboot

Details

The function toxboot takes performs bootstrap analysis on a single m4id included in the data.table supplied. This function acts as a wrapping and cleaning function around toxboot to both simplify setup with common defaults and to provide multicore support through the use of mclapply.

Value

dat, a data.table corresponding to the level 3 data for the aeids with columns added for m4id and bmad.

toxboot documentation built on Nov. 26, 2018, 1:04 a.m.