RnBeads (version 1.4.0)

get.comparison.info: get.comparison.info

Description

retrieve the comparison information for an RnBSet object

Usage

get.comparison.info(x, pheno.cols = rnb.getOption("differential.comparison.columns"), region.types = rnb.region.types.for.analysis(x), pheno.cols.all.pairwise = rnb.getOption("differential.comparison.columns.all.pairwise"), columns.pairs = rnb.getOption("columns.pairing"), columns.adj = rnb.getOption("covariate.adjustment.columns"), adjust.sva = rnb.getOption("differential.adjustment.sva"), pheno.cols.adjust.sva = rnb.getOption("inference.targets.sva"), adjust.celltype = rnb.getOption("differential.adjustment.celltype"), adjust.na.rm = TRUE)

Arguments

x

RnBSet object

pheno.cols

column names of the pheno slot in x on which the dataset should be partitioned. Those columns are required to be factors or logical. In case of factors, each group in turn will be compared to all other groups

region.types

which region types should be processed for differential methylation

pheno.cols.all.pairwise

integer or character vector specifying the colomns of pheno(x) on which all pairwise comparisons should be conducted. A value of NULL indicates no columns.

columns.pairs

argument passed on to rnb.sample.groups. See its documentation for details.

columns.adj

Column names or indices in the table of phenotypic information to be used for confounder adjustment in the differential methylation analysis.

adjust.sva

flag indicating whether the adjustment table should also contain surrogate variables (SVs) for the given target variable.

pheno.cols.adjust.sva

Target variables for SVA adjustment. Only important if adjust.sva==TRUE. Only the intersection of pheno.cols and pheno.cols.adjust.sva is considered for SVA adjustment.

adjust.celltype

flag indicating whether the resulting table should also contain estimated celltype contributions. See rnb.execute.ct.estimation for details.

adjust.na.rm

Flag indicating whether NAs in the adjustment table should be removed.

Value

a list containing one element for each comparison to be conducted. Each element is again a list containing:

comparison

the name of the comparison

pheno.colname

the column name of the sample annotation table the comparison is derived from

group.names

the names of the two groups being compared

group.inds

the sample indices of the samples belonging to the two groups

paired

flag indicating whether paired analysis is conducted

adj.sva

flag indicating whether adjustment for SVA is conducted

adj.celltype

flag indicating whether adjustment for cell type is conducted

adjustment.table

the covariate adjustment table. NULL if the comparison is not adjusted

region.types

the region types applicable to the analysis

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
cmp.info <- get.comparison.info(rnb.set.example,pheno.cols=c("Sample_Group","Treatment"))
cmp.info[[1]]