get.adjustment.variables: get.adjustment.variables

In RnBeads: RnBeads

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

Author(s)

Fabian Mueller

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")

RnBeads documentation built on March 3, 2021, 2 a.m.