summarize.clones {aCGH} | R Documentation |
Extracting summary information for all clones
Description
summarize.clones
function is the text equivalent of
plotFreqStat
function - it summarizes the frequencies of
changes for each clone accross tumors and when available assigns statistics. The resulting table can be easily exported.
Usage
summarize.clones(aCGH.obj, resT = NULL, pheno = rep(1, ncol(aCGH.obj)), rsp.uniq = unique(pheno), thres = 0.25, factor = 2.5, all = length(rsp.uniq) == 1 && is.null(resT), titles = if (all) "all" else rsp.uniq)
Arguments
aCGH.obj |
aCGH.obj object here
|
resT |
Data frame having the same structure as the result of
applying mt.maxT or mt.minP functions
from Bioconductor's multtest package for multiple testing.
The result is a data frame including the following 4 components:
'index', 'teststat', 'rawp' and 'adjp'.Default is the unique levels of the phenotype. Not used when all is TRUE.
|
pheno |
phenotype to compare
|
rsp.uniq |
rsp.uniq specified the codes for the groups of
interest. Default is the unique levels of the phenotype. Not used
when all is TRUE.
|
thres |
thres is either a vector providing unique
threshold for each sample or a vector of the same length as number
of samples (columns in data ) providing sample-specific
threshold. If aCGH.obj has non-null sd.samples , then threshold is automatically replaced by tumor-specific sd multiplied by factor . Clone is considered to be gained if it is above the
threshold and lost if it below negative threshold. Defaults to 0.25
|
factor |
factor specifies the number by which experimental variability should be multiples. used only when tumor specific variability in aCGH.obj is not NULL. Defaults to 2.5
|
all |
all specifies whether samples should be analyzed by subgroups (TRUE) or together (FALSE)
|
titles |
titles names of the groups to be used. Default is the unique levels of the pheno .
|
Value
Returns matrix containg the following information for each clones: annotation (same as in clones.info
), number and proportion of samples where clone is present,gained and lost; and the same in each group if more than one group. Additionally, if significance comparison has been done, value of the statistic, unadjusted p-value and adjusted p-values are included for each clone.
Author(s)
Jane Fridlyand
See Also
plotFreqStat
, aCGH
Examples
data(colorectal)
summarize.clones(colorectal)
[Package
aCGH version 1.62.0
Index]