RnBeads (version 1.4.0)

get.adjustment.variables: get.adjustment.variables

Description

Given indices for two groups of samples for comparison, this function retrieves data.frame containing the variables to be adjusted for

Usage

get.adjustment.variables(rnbSet, inds.g1, inds.g2 = -inds.g1, colnames.adj = c(), colname.target = "", adjust.sva = FALSE, adjust.celltype = FALSE)

Arguments

rnbSet

RnBSet object

inds.g1

sample indices in rnbSet of group 1 members

inds.g2

sample indices in rnbSet of group 2 members

colnames.adj

column names in pheno(rnbSet) to retrieve

colname.target

column names in pheno(rnbSet) of the target variable. Only important if adjust.sva==TRUE

adjust.sva

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

adjust.celltype

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

Value

a data.frame containing one column for each selected variable from the phenotypic data each row corresponds to a sample in the union of samples of the wto groups with the first length(inds.g1) rows corresponding to group 1 and the remaining rows corresponding to group 2

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
sample.groups <- rnb.sample.groups(rnb.set.example)[[1]]
get.adjustment.variables(rnb.set.example,sample.groups[[1]],sample.groups[[2]],"Cell_Line")