comet.list: List the correlations between omic features

Description

coMET is an R-based package to visualize EWAS (epigenome-wide association scans) results in a genomic region of interest. The main feature of coMET is to plot the the significance level of EWAS results in the selected region, along with correlation in DNA methylation values between CpG sites in the region. The coMET package generates plots of phenotype-association, co-methylation patterns, and a series of annotation tracks. In addition, the function comet.list gives the list of correlations between omic features

Usage

comet.list(cormatrix.file = NULL, cormatrix.method = "spearman", cormatrix.format = "raw",  cormatrix.conf.level=0.05, cormatrix.sig.level= 1, cormatrix.adjust="none",  cormatrix.type = "listdataframe", cormatrix.output="cormatrix_list", config.file = NULL, verbose = FALSE)

Arguments

cormatrix.file

Name of the raw data file or the pre-computed correlation matrix file. It is mandatory and has to be a file in tabular format with an header.

cormatrix.method

Options for calculating the correlation matrix: spearman, pearson and kendall. Default value= spearman

cormatrix.format

Format of the input cormatrix.file. TThere are two options: raw file (raw if CpG sites are by column and samples by row or raw_rev if CpG site are by row and samples by column) and pre-computed correlation matrix (cormatrix)

cormatrix.conf.level

Alpha level for the confidence interval. Default value= 0.05. CI will be the alpha/2 lower and upper values.

cormatrix.sig.level

Significant level to visualise the correlation. If the correlation has a pvalue below the significant level, the correlation will be colored in "goshwhite", else the color is related to the correlation level and the color scheme choosen.Default value =1.

cormatrix.adjust

indicates which adjustment for multiple tests should be used. "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".Default value="none"

cormatrix.type

Format of cormatrix.file. There are 2 different options: listfile or listdataframe.

cormatrix.output

The path and the name of the output file without the extension

config.file

Configuration file contains the values of these options instead of defining these by command line. It is a file where each line is one option. The name of option and its value are separated by "=".

verbose

logical option TRUE or FALSE. TRUE (default). If TRUE, shows comments.

Value

Create a list of correlation between omic features

References

http://epigen.kcl.ac.uk/comet/

Examples

Run this code

extdata <- system.file("extdata", package="coMET",mustWork=TRUE)
mycorrelation <- file.path(extdata, "cyp1b1_res37_rawMatrix.txt")
myoutput <- file.path(extdata, "cyp1b1_res37_cormatrix_list_BH05.txt")


comet.list(cormatrix.file=mycorrelation,cormatrix.method = "spearman",
           cormatrix.format= "raw", cormatrix.conf.level=0.05,
           cormatrix.sig.level= 0.05, cormatrix.adjust="BH",
           cormatrix.type = "listfile", cormatrix.output=myoutput, 
           verbose=FALSE)