Description Usage Arguments Details Value Author(s) References Examples
This function computes permutation t-tests for differences in each line of a matrix between consecutive levels of an ordered grouping variable.
1 |
data |
a numeric matrix, for the lines of which we want to test the null of no trend across groups |
g |
integer vector with group labels for the ordered categories coded as integers between 1 and n, where n is the number of ordered categories |
B |
number of permutations or a list of permutation matrices |
rep |
integer vector with group labels ranging from 1 to m where m is the number of independent samples (e.g. individuals). The ordering is not important. |
pttest takes a matrix and for each line computes a permutation t-test
between consecutive levels of an ordered grouping variable. Random
factors e.g. technical replicates can be specified and will be accounted
for by permuting samples only within independent units of this
factor. A matrix with raw permutation p-values as well as a matrix with
the directional decisions are returned. See guo
and
sigdirPttest
for a way to get
test decisions with control over the mixed directional false discovery
rate.
raw |
matrix with raw p.values |
dir |
matrix with the direction of each decision |
Florian Klinglmueller <float_at_lefant.net>
Klinglmueller, F., Tuechler, T., Posch, M. (2010) "Cross Platform Comparison Of Microarray Data Using Order Restricted Inference" Under Review
Guo W., Sarkar SK., Peddada SD. (2010) "Controlling False Discoveries in Multidimensional Directional Decisions, with Applications to Gene Expression Data on Ordered Categories" Biometrics
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