diffmean {TCGAbiolinks} | R Documentation |
Calculate diffmean methylation of probes between two groups removing lines that has NA values.
diffmean(data, groupCol = NULL, group1 = NULL, group2 = NULL, save = FALSE)
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 |
Saves in the rowRages(data) the columns: mean.group1, mean.group2 diffmean.group1.group2; Where group1 and group2 are the names of the groups.
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")