readEH: A wrapper function for efficiently reading in user-specified...

In dozmorovlab/preciseTADhub: Pre-trained random forest models obtained using preciseTAD

Description

A wrapper function for efficiently reading in user-specified random forest models generated by preciseTAD::TADrandomForest, built on cell-line specific CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peak regions.

Usage

readEH(chr, cl, gt, source)

Arguments

chr	Which chromosome was used as the holdout during the training process. That is, all other chromosomes were combined when building the random forest.
cl	The cell line that was used (either "GM12878" or "K562")
gt	The ground-truth TAD or chromatin loop boundaries used to construct the binary response vector (either "Arrowhead" or "Peakachu".
source	The source of the files stored on ExperimentHub using query(hub, "package_name").

Value

A trained model object from caret

Examples

# Suppose we want to read in the model that was built using CHR1-CHR21,
# on GM12878, using Arrowhead defined TAD boundaries at 5kb resolution.

#Initialize ExperimentHub
library(ExperimentHub)
hub <- ExperimentHub()
query(hub, "preciseTADhub")
myfiles <- query(hub, "preciseTADhub")

CHR22_GM12878_5kb_Arrowhead <- readEH(chr = "CHR22",
                                      cl = "GM12878",
                                      gt = "Arrowhead",
                                      source = myfiles)

dozmorovlab/preciseTADhub documentation built on Aug. 14, 2021, 8:19 p.m.