geneByMeth: Correlate methylation and gene expression data.

Description Usage Arguments Details Value Author(s)

Description

Get genes within a 1 Mb region centered on a methylation region and fit linear models with methylation status as independent variable and gene expression as dependent variable

Usage

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geneByMeth(tab, genes, eset, samps, gene.data, chip.db = NULL, contname,
  dontuse = "", orgpkg, stratifyBySex = FALSE, extra.indeps = NULL)

Arguments

tab

A data.frame containing the chromosome, start, stop for a methylation region. Usually extracted from the table list item of a 'bumps' object.

genes

A GRanges object that lists known genes. Usually generated by e.g. genes(TxDb.Hsapiens.UCSC.hg19.knownGene)

eset

Usually a GenomicRatioSet, created by a call to preprocessQuantile from the mimfi package

samps

A data.frame that maps samples to phenotype. This data.frame MUST contain columns named Category and Gender!

gene.data

Default is NULL. Otherwise, a data.frame or matrix containing gene expression data. The columns of this data.frame must correspond exactly to columns of the methylation data. Row names must be array IDs or Entrez gene IDs.

chip.db

The chip-level array data package corresponding to the gene expression data. If NULL, the assumption will be made that the row.names are ENTREZ GENE IDs.

contname

A contrast name, used to name the directory where these data will be stored. Usually of the form 'this_vs_that'.

dontuse

Which Categories from the samps data.frame should we NOT use? If only two Category levels, use "".

orgpkg

An organism level annotation package (e.g., Homo.sapiens)

stratifyBySex

Boolean. Do you want to stratify the plots by sex? Defaults to FALSE.

extra.indeps

Extra independent variables for the model of gene expression regressed on methylation status. These must conform to column names of the samps data.frame.

Details

This function takes a table of differentially methylated regions, selects the genes that are within 1 Mb of a given region, and then fits models that test for a relationship between methylation status and gene expression. In order for this to work correctly the gene expression and methylation data must be in corresponding columns (e.g., sample 1 must be in the first column of the methylation data as well as the expression data). In addition, the row.names of the gene expression data have to be the manufacturer IDs, so we can figure out what genes are being interrogated. Otherwise, the row.names can be ENTREZ GENE IDs.

Value

This function returns a list of HTMLReportRef items that can be used to create links.

Author(s)

James W. MacDonald ([email protected])


jmacdon/methylation documentation built on May 19, 2019, 12:49 p.m.