get.adjustment.variables {RnBeads} | R Documentation |
Given indices for two groups of samples for comparison, this function
retrieves data.frame
containing the variables to be adjusted for
get.adjustment.variables(rnbSet, inds.g1, inds.g2 = -inds.g1, colnames.adj = c(), colname.target = "", adjust.sva = FALSE, adjust.celltype = FALSE)
rnbSet |
RnBSet object |
inds.g1 |
sample indices in |
inds.g2 |
sample indices in |
colnames.adj |
column names in |
colname.target |
column names in |
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 |
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
Fabian Mueller
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")