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

Description Usage Arguments See Also Examples

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

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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

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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 May 2, 2020, 2:01 a.m.