R package for reading in and working with NucleoATAC outputs. This package doesn't replicate what NucleoATAC does-- just makes it easier to read in the outputs from NucleoATAC for visualizing and post-processing analysis in R.
Also includes functions for finding +1 and -1 nucleosomes, finding distances between nucleosomes, and plotting V-plots.
Install using devtools:
devtools::install_github("GreenleafLab/NucleoATACR")Load:
library(NucleoATACR)Read in nucleosome and nfr positions:
nucs <- readNucs("test.nucmap_combined.bed.gz")
nfrs <- readNFRs("test.nfrpos.bed.gz")Read in nucleoatac signal track for particular locus:
signal <- readBedgraph("test.nucleoatac_signal.bedgraph.gz", "chrII", 706551, 707705)Read in vplot and plot:
v <- read_vplot("test.VMat")
plotV(v)Get +1 and -1 nucleosomes:
fake_tss <- GenomicRanges::GRanges("chrII", IRanges::IRanges(start = c(707200,707500), width = 1),
strand = c("+","-"))
p1 <- get_p1_nuc(nucs.ranges = nucs, sites = fake_tss)
m1 <- get_m1_nuc(nucs.ranges = nucs, sites = fake_tss)