as_profileplyr

Argument	Description
chipProfile	A ChIPprofile object as created by the ‘regionPlot’ funtion within the soGGi package
testRanges	A character vector with paths to BED files.
names	Column to select row IDs/names from ChIPprofile mcols.

Example

• The ‘BamBigwig_to_chipProfile’ function uses the soGGi package from Bioconductor
• It requires paths to one or multiple signal files (either bigwig or bam file) and bed files
• This can take a while with lots of ranges (how long?) so we will load a pre-complied object

Assign path to bed file to a variable

testRanges <- "K27ac_top10_HUES64.bed"

---

Read in the paths to the signal files (either bigwig or BAM files)

• To get bigwig files, go here
• Scroll/search for samples E016 (stem cells) and E013 (mesoderm) and download H3K27ac, H3K4me1, and H3K4me3 for each sample
• if this becomes a talk, need to probably shrink these and put into data people can access

library(profileplyr)
library(grid)

esc_files <- list.files("HUES64_E016/", full.names = TRUE)
meso_files <- list.files("meso_HUES64_E013/", full.names = TRUE)

esc_bigwigs <- esc_files[grepl("bigwig", esc_files)]
meso_bigwigs <- meso_files[grepl("bigwig", meso_files)]

signalFiles <- c(esc_bigwigs, meso_bigwigs)

---

Quantify bigwig signal over peaks in bed file

• Quantify the signal with ‘BamBigwig_to_chipProfile’ function (makes a chipProfile object from soGGi package)
• Convert chipProfile object to profileplyr object

# chunk not evaluated
chipProfile <- BamBigwig_to_chipProfile(signalFiles = signalFiles, 
                         testRanges = testRanges, 
                         format = "bigwig", 
                         style = "percentOfRegion",
                         nOfWindows = 50,
                         distanceAround = 100)

# Convert this output to profileplyr object
proplyr_object <- as_profileplyr(chipProfile)