COHCAP.integrate.avg.by.island: Integration with Gene Expression Data(Average by Island...

In COHCAP: CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Description

Provides lists of genes with a significant negative correlation between DNA methylation and gene expression data.

A table of normalizated intensity / expression values is provided in the gene expression table and a table of filtered beta values is provided for the DNA methylation data.

Lists of genes with negative expression trends will be created in the "Integrate" folder, along with scatter plots (if descired). All correlation stats are provided in the "Raw_Data" folder.

Usage

COHCAP.integrate.avg.by.island(island.list, project.name, project.folder,
				expr.file, sample.file, cor.pvalue.cutoff=0.05,
				cor.fdr.cutoff = 0.05, cor.cutoff = -0.2, plot.scatter=TRUE,
				output.format = "txt", ref="none")

Arguments

island.list	list with two data frames: island.list$filtered.island.stats = differential methylation results for CpG Islands island.list$beta.table = Data frame with beta values averaged across differentially methylated sites (islands in rows, samples in columns). This table is already filtered for differentially methylated CpG islands. The COHCAP.avg.by.island function automatically creates this file.
project.name	Name for COHCAP project. This determines the names for output files.
project.folder	Folder for COHCAP output files
expr.file	Table of normalized expression or intensity values (can be for either microarray or RNA-Seq data). Sample IDs (listed in column header) must match the sample IDs used for the DNA methylation data (e.g. those listed in beta.table)
sample.file	Tab-delimited text file providing group attributions for all samples considered for analysis. Only used if plot.scatter=TRUE
cor.cutoff	The minimum negative correlation coefficient to define a differentially expressed gene.
cor.pvalue.cutoff	Maximum p-value allowed to define a gene as differentially expressed.
cor.fdr.cutoff	Maximum False Discovery Rate (FDR) allowed to define a gene as differentially expressed.
plot.scatter	A logical value: Create scatter plot for genes with a significant negative correlation?
output.format	Format for output tables: 'xls' for Excel file, 'csv' for comma-separated file, or 'txt' for tab-delimited text file
ref	Describes reference setting for upstream analysis. If creating scatterplots, checks if ref="continuous" (changing plots from discrete to continuous color scale)

See Also

COHCAP Discussion Group: http://sourceforge.net/p/cohcap/discussion/general/

Examples

library("COHCAP")

dir = system.file("extdata", package="COHCAP")
beta.file = file.path(dir,"GSE42308_truncated.txt")
sample.file = file.path(dir,"sample_GSE42308.txt")
project.folder = tempdir()#you may want to use getwd() or specify another folder
expression.file = file.path(dir,"expression-Average_by_Island_truncated.txt")
project.name = "450k_avg_by_island_test"

beta.table = COHCAP.annotate(beta.file, project.name, project.folder,
				platform="450k-UCSC")
filtered.sites = COHCAP.site(sample.file, beta.table, project.name,
				project.folder, ref="parental")
island.list = COHCAP.avg.by.island(sample.file, filtered.sites,
				beta.table, project.name, project.folder, ref="parental")
COHCAP.integrate.avg.by.island(island.list, project.name,
				project.folder, expression.file, sample.file)

COHCAP documentation built on Nov. 8, 2020, 8:07 p.m.