diffmean {TCGAbiolinks}R Documentation

Calculate diffmean methylation between two groups

Description

Calculate diffmean methylation of probes between two groups removing lines that has NA values.

Usage

diffmean(data, groupCol = NULL, group1 = NULL, group2 = NULL,
  save = FALSE)

Arguments

data

SummarizedExperiment object obtained from TCGAPrepare

groupCol

Columns in colData(data) that defines the groups.

group1

Name of group1 to be used in the analysis

group2

Name of group2 to be used in the analysis

save

Save histogram of diffmean

Value

Saves in the rowRages(data) the columns: mean.group1, mean.group2 diffmean.group1.group2; Where group1 and group2 are the names of the groups.

Examples

nrows <- 200; ncols <- 20
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GenomicRanges::GRanges(rep(c("chr1", "chr2"), c(50, 150)),
                   IRanges::IRanges(floor(runif(200, 1e5, 1e6)), width=100),
                    strand=sample(c("+", "-"), 200, TRUE),
                    feature_id=sprintf("ID%03d", 1:200))
colData <- S4Vectors::DataFrame(Treatment=rep(c("ChIP", "Input"), 10),
                    row.names=LETTERS[1:20],
                    group=rep(c("group1","group2"),c(10,10)))
data <- SummarizedExperiment::SummarizedExperiment(
         assays=S4Vectors::SimpleList(counts=counts),
         rowRanges=rowRanges,
         colData=colData)
 diff.mean <- TCGAbiolinks:::diffmean(data,groupCol = "group")
[Package TCGAbiolinks version 2.6.12 Index]