COHCAP.integrate.avg.by.site: Integration with Gene Expression Data(Average by Site...

In cwarden45/COHCAP: CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data

Integration with Gene Expression Data(Average by Site Workflow).

Description

Provides lists of genes with an inverse CpG island methylation trend (Methylation Down, Expression Up and Methylation Up, Expression Down).

Lists of genes with negative expression trends will be created in the "Integrate" folder.

The "Average by Site" workflow requires that genes already have fold-change, p-value, and FDR values calculated. There many tools available for this type of analysis (limma, DEseq2, edgeR, etc.)

This function will only work for 2-group comparisons.

Usage

COHCAP.integrate.avg.by.site(island.table, project.name, project.folder,
				expr.file, expr.pvalue=0.05, expr.fdr = 0.05, expr.fc = 1.5,
				output.format = "txt")

Arguments

island.table	Data frame with CpG island statistics (one row per CpG island) for differentially methylated CpG islands. The COHCAP.avg.by.site 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 differential expression statistics. Gene symbols must be in the first column, fold-change values must be in the second column, p-values must be in the third column, and false discovery rate (FDR) values must be in the fourth column. These statistics must be calculated outside of COHCAP. Duplicate gene symbols are OK - statistics will be averaged among duplicate gene symbols.
expr.fc	The minimum absolute value for fold-change values (treatment versus reference) to define gene as differentially expressed (from gene expression table). Only used for 2-group comparison. Fold-change is expected to be on a linear scale.
expr.pvalue	Maximum p-value allowed to define a gene as differentially expressed (from gene expression table).
expr.fdr	Maximum False Discovery Rate (FDR) allowed to define a gene as differentially expressed (from gene expression table)
output.format	Format for output tables: 'xls' for Excel file, 'csv' for comma-separated file, or 'txt' for tab-delimited text file

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_Site_truncated.txt")
project.name = "450k_avg_by_site_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")
filtered.islands = COHCAP.avg.by.site(filtered.sites, project.name,
				project.folder)
COHCAP.integrate.avg.by.site(filtered.islands, project.name, project.folder,
				expression.file)

cwarden45/COHCAP documentation built on April 16, 2024, 3:17 a.m.