readTFBSdb: Read BED file of TFBS scores into GRange object

In GabrielHoffman/tfbsDB: Store and plot TFBS sites from HOCOMOCO v11 scored by FIMO

Description

Read BED file of TFBS scores into GRange object

Usage

readTFBSdb(grQuery, bedFile, maxP = 1e-04, quality = c("A", "B", "C"))

Arguments

grQuery	GRange object of query interval
bedFile	BED file that is bgzipped and tabix'd.
maxP	maximum p-value of TFBS returned
quality	each motif has a quality value in c('A', 'B', 'C', 'D'). But default exclude quality D, the lowest quality motifs

Value

GRange of TFBS locations where p-values are scores

Examples

library(GenomicRanges)
library(tfbsDB)

# range of TFBS to be loaded from file
grQuery = GRanges("chr1", IRanges(10280, 10410))

# example data from package
bedFile = file.path(system.file("extdata/", package = "tfbsDB"), "hocomocov11_hg19_example.bed.gz")

# read from file
gr = readTFBSdb( grQuery, bedFile )

# show TFBS locations
plotTFBSdb( gr )

# color locations by p-value of motif match
plotTFBSdb( gr, colorByP=TRUE)

GabrielHoffman/tfbsDB documentation built on June 23, 2020, 5:29 a.m.