cpg_analysis {HodgesTools} | R Documentation |
CpG Analysis
Description
Compute observed/expected CpG ratio and GC% for regions of interest
Usage
cpg_analysis(
list = FALSE,
count,
cpg_file,
nuc_file,
palette = "Set3",
plot = "none"
)
Arguments
list |
"boolean of whether input is a list of groups. Default = FALSE." |
count |
"numeric value for the number of files included in your list |
cpg_file |
"file names or list of files names for your CpGcount.txt files. This is defined in cpg_analysis.sh" |
nuc_file |
"file names or list of files names for your nucOutput_gc.txt files. This is defined in cpg_analysis.sh" |
palette |
"if choosing to plot, the RColorBrewer palette you would like to be applied to your plot" |
plot |
"one of three choices depending on what output you would like: 'none' for no plot, 'ratio' for observed/expected ratios, 'gc_percent' for GC%" |
Details
The function reads in a nucOutput_gc and CpGcount text file The function uses the nucOutput_gc and CpGcount file to calculates observed/expected ratio and GC%. The function allows the option to plot the distribution of these values in ggplot2
Value
ggplot object or tibble if plot="none"
Author(s)
Lindsey Guerin
Examples
#load external data
gain_6hr_CpG <- system.file(package = "HodgesTools", "extdata",
"cov5root_6hr_gain.CpGcount.txt")
gain_12hr_CpG <- system.file(package = "HodgesTools", "extdata",
"cov5root_12hr_gain.CpGcount.txt")
gain_6hr_nuc <- system.file(package = "HodgesTools", "extdata",
"cov5root_6hr_gain.nucOutput_gc.txt")
gain_12hr_nuc <- system.file(package = "HodgesTools", "extdata",
"cov5root_12hr_gain.nucOutput_gc.txt")
#Make a density plot of GC% values for a list of two region of interest files
cpg_analysis(list = TRUE, count = 2, cpg_file = list(gain_6hr_CpG, gain_12hr_CpG),
nuc_file= list(gain_6hr_nuc, gain_12hr_nuc), palette = "Set3", plot ="gc_percent")
#Make a density plot of observed/expected values for a single set of regions of interest
cpg_analysis(list = FALSE, cpg_file = gain_6hr_CpG,
nuc_file = gain_6hr_nuc, palette = "Set3", plot ="ratio")