plotAndOut: Create tables and plots showing correlation between...

Description Usage Arguments Details Value Author(s)

Description

A function to create tables showing correlation between methylation status and gene expression.

Usage

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plotAndOut(lstitm, eset, prb, samps, file, contname, orgpkg,
  stratifyBySex = FALSE, extra.indeps = NULL)

Arguments

lstitm

A data.frame containing gene expression data for genes that are within the 1 Mb region centered on the methylation 'bump'.

eset

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

prb

A vector of probe IDs that correspond to the differently methylated (Illumina 450K) probe IDs.

samps

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

file

A filename. In general this is the genomic region, separated by underscores (e.g., chr1_12345_23456)

contname

A contrast name. Usually this is lowercase and separated by underscores (e.g., this_vs_that)

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

Additional independent variables to use when fitting the model regressing methylation on gene expression. These must conform to column names of the samps data.frame.

Details

This function is not intended to be called by the end user. Instead it is intended to create the HTML table showing correlation between gene gene expression and methylation status, as well as xyplots that show the correlation graphically.

Value

This returns an HTMLReportRef.

Author(s)

James W. MacDonald ([email protected])


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